- P - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- P - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- P - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- p - Variable in class etomica.box.RandomPositionSourceDeformable
-
- p - Variable in class etomica.box.RandomPositionSourceRectangular
-
- p - Variable in class etomica.normalmode.MeterDDP
-
- p - Variable in class etomica.normalmode.MeterDP
-
- p - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- P - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- P - Variable in class etomica.potential.P2HePCKLJS
-
- p - Variable in class etomica.potential.P2HydrogenPatkowski
-
- p - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- p - Variable in class etomica.potential.PotentialAtomicSum
-
- p - Variable in class etomica.potential.PotentialMolecularSum
-
- p - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- p - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- p - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- p - Variable in class etomica.virial.cluster.VirialDiagrams
-
- p - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- p - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- p - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- p - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- p - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- P - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- p - Variable in class etomica.virial.PotentialNonAdditive
-
- p0 - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- P0LatticeEnergyCorrec - Class in etomica.models.nitrogen
-
The lattice energy correction for Nitrogen model
zero-body interaction
All the parameters are determined from the fitted equation.
- P0LatticeEnergyCorrec(ISpace) - Constructor for class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- P0Lrc(ISpace, Potential2Soft, Potential2Soft, IAtomType[]) - Constructor for class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- P0ReactionField(ISpace, P2ReactionFieldDipole) - Constructor for class etomica.potential.P2ReactionFieldDipole.P0ReactionField
-
- P0ReactionField(ISpace, P2ReactionFieldDipoleTruncated) - Constructor for class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomNPath
-
- p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- p1 - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- p1 - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- p1 - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- p1 - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- p1 - Variable in class etomica.normalmode.MeterDDP
-
- p1 - Variable in class etomica.normalmode.MeterDP
-
- p1 - Variable in class etomica.normalmode.MeterTargetTP
-
- p1 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- p1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- p1 - Variable in class etomica.virial.ClusterExchange
-
- p1 - Variable in class etomica.virial.P1IntraLambda
-
- p1BoundaryA - Variable in class etomica.modules.mu.Mu
-
- p1BoundaryB - Variable in class etomica.modules.mu.Mu
-
- p1Constraint - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- P1Constraint - Class in etomica.normalmode
-
- P1Constraint(ISpace, double, IBox, CoordinateDefinition) - Constructor for class etomica.normalmode.P1Constraint
-
- p1Constraint - Variable in class etomica.normalmode.SimCalcSLJ
-
- p1Constraint - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- p1Constraint - Variable in class etomica.normalmode.SimOverlapLJ
-
- p1Constraint - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- p1Constraint - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- P1ConstraintNbr - Class in etomica.normalmode
-
- P1ConstraintNbr(ISpace, double, ISimulation) - Constructor for class etomica.normalmode.P1ConstraintNbr
-
- P1ConstraintNbr(ISpace, double, ISimulation, double) - Constructor for class etomica.normalmode.P1ConstraintNbr
-
- P1ConstraintNbrHcp - Class in etomica.normalmode
-
- P1ConstraintNbrHcp(ISpace, double, IBox) - Constructor for class etomica.normalmode.P1ConstraintNbrHcp
-
- p1Counter - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- P1ExternalField - Class in etomica.potential
-
- P1ExternalField(ISpace) - Constructor for class etomica.potential.P1ExternalField
-
- P1HardBoundary - Class in etomica.potential
-
Potential that places hard repulsive walls coinciding with the
boundary of the box, which is assumed to be rectangular in shape.
- P1HardBoundary(ISpace) - Constructor for class etomica.potential.P1HardBoundary
-
- P1HardBoundary(ISpace, boolean) - Constructor for class etomica.potential.P1HardBoundary
-
- P1HardMovingBoundary - Class in etomica.potential
-
Potential that places hard repulsive walls that move and
accelerate subject to an external force field (pressure).
- P1HardMovingBoundary(ISpace, IBoundary, int, double, boolean) - Constructor for class etomica.potential.P1HardMovingBoundary
-
Constructor for a hard moving (and accelerating) boundary.
- P1HardPeriodic - Class in etomica.potential
-
pseudo-potential for a "collision" time to update colliders for periodic boundaries
- P1HardPeriodic(ISpace) - Constructor for class etomica.potential.P1HardPeriodic
-
Returns an instance of P1HardPeriodic with sigma = NaN.
- P1HardPeriodic(ISpace, double) - Constructor for class etomica.potential.P1HardPeriodic
-
Returns an instance of P1HardPeriodic with the given value of sigma (the
maximum distance between two atoms where they interact)
- P1HardWall - Class in etomica.modules.osmosis
-
- P1HardWall(ISpace) - Constructor for class etomica.modules.osmosis.P1HardWall
-
- P1HardWall(ISpace, double) - Constructor for class etomica.modules.osmosis.P1HardWall
-
- P1Harmonic - Class in etomica.potential
-
Potential in which attaches a harmonic spring between each affected atom and
the nearest boundary in each direction.
- P1Harmonic(ISpace) - Constructor for class etomica.potential.P1Harmonic
-
- P1HarmonicSite - Class in etomica.potential
-
Potential in which attaches a harmonic spring between each affected atom a
nominal site for that atom, as defined by an agent manager.
- P1HarmonicSite(ISpace) - Constructor for class etomica.potential.P1HarmonicSite
-
- P1HydrogenMielke - Class in etomica.potential
-
- P1HydrogenMielke(ISpace) - Constructor for class etomica.potential.P1HydrogenMielke
-
- P1HydrogenMielke.P1HydrogenMielkeAtomic - Class in etomica.potential
-
- P1HydrogenMielke.P2HydrogenMielkeAtomic - Class in etomica.potential
-
- P1HydrogenMielkeAtomic(ISpace) - Constructor for class etomica.potential.P1HydrogenMielke.P1HydrogenMielkeAtomic
-
- P1ImageHarmonic - Class in etomica.freeenergy.npath
-
Created by andrew on 4/11/17.
- P1ImageHarmonic(ISpace, IVector, double) - Constructor for class etomica.freeenergy.npath.P1ImageHarmonic
-
- p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimLJ
-
- p1Intra - Variable in class etomica.modules.sam.Sam
-
- P1IntraLambda - Class in etomica.virial
-
- P1IntraLambda(ISpace, double, P1IntraMolecular, double) - Constructor for class etomica.virial.P1IntraLambda
-
- P1IntraMolecular - Interface in etomica.potential
-
- P1IntraSimple - Class in etomica.potential
-
Generic intramolecular potential group, having one potential for bonded
atoms, and a different potential for unbonded ones.
- P1IntraSimple() - Constructor for class etomica.potential.P1IntraSimple
-
- P1LepsHarmonic - Class in etomica.dimer
-
A combination of the basic LEPS potential describing 3 atoms moving in 1-dimension, paired with a harmonic potential.
- P1LepsHarmonic(ISpace) - Constructor for class etomica.dimer.P1LepsHarmonic
-
- P1MagicWall - Class in etomica.modules.mu
-
- P1MagicWall(ISpace, PotentialMasterList) - Constructor for class etomica.modules.mu.P1MagicWall
-
- P1MagneticField - Class in etomica.spin
-
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
- P1MagneticField(ISpace) - Constructor for class etomica.spin.P1MagneticField
-
- P1Sinusoidal - Class in etomica.modules.sam
-
- P1Sinusoidal(ISpace) - Constructor for class etomica.modules.sam.P1Sinusoidal
-
- p1Smash - Variable in class etomica.modules.droplet.Droplet
-
- p1Smash - Variable in class etomica.modules.droplet.DropletAtomic
-
- P1Smash - Class in etomica.modules.droplet
-
Gravity-like potential that pushes the molecules toward the center.
- P1Smash(ISpace) - Constructor for class etomica.modules.droplet.P1Smash
-
- P1SoftBoundary - Class in etomica.potential
-
- P1SoftBoundary(ISpace) - Constructor for class etomica.potential.P1SoftBoundary
-
- P1SoftBoundary(ISpace, double) - Constructor for class etomica.potential.P1SoftBoundary
-
- p1SurfaceBond - Variable in class etomica.modules.sam.Sam
-
- p1Tension - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- P1Tension - Class in etomica.modules.materialfracture
-
- P1Tension(ISpace) - Constructor for class etomica.modules.materialfracture.P1Tension
-
- P1Tether - Class in etomica.modules.rosmosis
-
Potential for a harmonic tether.
- P1Tether(IBox, ISpecies, ISpace) - Constructor for class etomica.modules.rosmosis.P1Tether
-
- P1Wall - Class in etomica.interfacial
-
- P1Wall(ISpace, double, double, double) - Constructor for class etomica.interfacial.P1Wall
-
- P1Wall - Class in etomica.modules.adsorption
-
- P1Wall(ISpace) - Constructor for class etomica.modules.adsorption.P1Wall
-
- P1Wall - Class in etomica.modules.colloid
-
- P1Wall(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P1Wall
-
- p1WallA - Variable in class etomica.modules.adsorption.Adsorption
-
- p1WallA - Variable in class etomica.modules.mu.Mu
-
- p1WallB - Variable in class etomica.modules.adsorption.Adsorption
-
- p1WallB - Variable in class etomica.modules.mu.Mu
-
- p1WallColloid - Variable in class etomica.modules.colloid.ColloidSim
-
- p1WallMonomer - Variable in class etomica.modules.colloid.ColloidSim
-
- P1WCAPorousWall - Class in etomica.modules.dcvgcmd
-
This acts as a 1-body WCA potential wall perpendicular to the z direction
with a hole.
- P1WCAPorousWall(ISpace) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- P1WCAPorousWall(ISpace, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- P1WCAWall - Class in etomica.modules.dcvgcmd
-
1-D potential that has a WCA form in the Z direction.
- P1WCAWall(ISpace, int) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
-
- P1WCAWall(ISpace, int, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
-
- P1WCAWall - Class in etomica.modules.sam
-
1-D potential that has a WCA form in the Z direction.
- P1WCAWall(ISpace, int) - Constructor for class etomica.modules.sam.P1WCAWall
-
- P1WCAWall(ISpace, int, double, double) - Constructor for class etomica.modules.sam.P1WCAWall
-
- p2 - Variable in class etomica.mappedvirial.MeterMeanForce
-
- p2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- p2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- p2 - Variable in class etomica.metastable.MeterDensityDistribution
-
- p2 - Variable in class etomica.modules.adsorption.ModifierPMu
-
- p2 - Variable in class etomica.modules.droplet.Droplet
-
- p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- p2 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- p2 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- p2 - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- p2 - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- P22CLJQ - Class in etomica.potential
-
Two-centered Lennard Jones molecule with a quadrupole.
- P22CLJQ(ISpace) - Constructor for class etomica.potential.P22CLJQ
-
- P22CLJQ(ISpace, double, double, double) - Constructor for class etomica.potential.P22CLJQ
-
- p2AA - Variable in class etomica.modules.adsorption.Adsorption
-
- p2AA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- p2AA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- p2AB - Variable in class etomica.modules.adsorption.Adsorption
-
- p2AB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- P2AceticAcidTwoSite - Class in etomica.models.OPLS
-
- P2AceticAcidTwoSite(double, boolean, int) - Constructor for class etomica.models.OPLS.P2AceticAcidTwoSite
-
- P2Anharmonic - Class in etomica.potential
-
Harmonic Well interatomic potential.
- P2Anharmonic(ISpace, double) - Constructor for class etomica.potential.P2Anharmonic
-
- P2ArgonAziz1993 - Class in etomica.potential
-
Pair potential for argon from Aziz (1993) JCP 99(6): 4518.
- P2ArgonAziz1993(ISpace) - Constructor for class etomica.potential.P2ArgonAziz1993
-
- P2ArgonSlavicekEtAl2003 - Class in etomica.potential
-
Ab initio pair potential for argon from Slavicek et al.
- P2ArgonSlavicekEtAl2003(ISpace) - Constructor for class etomica.potential.P2ArgonSlavicekEtAl2003
-
- P2ArgonTangAndToennies2003 - Class in etomica.potential
-
Pair potential for argon from Tang and Toennies 2003.
- P2ArgonTangAndToennies2003(ISpace) - Constructor for class etomica.potential.P2ArgonTangAndToennies2003
-
- p2BB - Variable in class etomica.modules.adsorption.Adsorption
-
- p2BB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- p2BB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- p2Bond - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2BondCC - Variable in class etomica.modules.sam.Sam
-
- p2BondCS - Variable in class etomica.modules.sam.Sam
-
- p2CH2 - Variable in class etomica.modules.sam.Sam
-
- p2CH2CH3 - Variable in class etomica.modules.sam.Sam
-
- p2CH2CH3t - Variable in class etomica.modules.sam.Sam
-
- p2CH2Surface - Variable in class etomica.modules.sam.Sam
-
- p2CH2t - Variable in class etomica.modules.sam.Sam
-
- p2CH3 - Variable in class etomica.modules.sam.Sam
-
- p2CH3t - Variable in class etomica.modules.sam.Sam
-
- p2Classy - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- p2Classy - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
-
- p2Classy - Variable in class etomica.potential.P2SemiclassicalAtomic
-
- p2Classy - Variable in class etomica.potential.P2SemiclassicalMolecular
-
- P2CO2EMP - Class in etomica.potential
-
3-point potential for CO2.
- P2CO2EMP(ISpace, double, double, double, double, double, double, double) - Constructor for class etomica.potential.P2CO2EMP
-
- P2CO2EMP1 - Class in etomica.potential
-
EPM model for CO2.
- P2CO2EMP1(ISpace) - Constructor for class etomica.potential.P2CO2EMP1
-
- P2CO2EMP2 - Class in etomica.potential
-
EPM2 model for CO2
- P2CO2EMP2(ISpace) - Constructor for class etomica.potential.P2CO2EMP2
-
- P2CO2H2OSC(double) - Constructor for class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- P2CO2H2OSCTI(double) - Constructor for class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- P2CO2H2OWheatley - Class in etomica.models.co2
-
Ab initio potential for CO2-H2O by Wheatley and Harvey
http://dx.doi.org/10.1063/1.3574345
The CO2 molecule is expected first
- P2CO2H2OWheatley(ISpace) - Constructor for class etomica.models.co2.P2CO2H2OWheatley
-
- P2CO2H2OWheatley.P2CO2H2OSC - Class in etomica.models.co2
-
- P2CO2H2OWheatley.P2CO2H2OSCTI - Class in etomica.models.co2
-
- P2CO2Hellmann - Class in etomica.models.co2
-
Ab initio potential for CO2-CO2 developed by R.
- P2CO2Hellmann(ISpace, P2CO2Hellmann.Parameters) - Constructor for class etomica.models.co2.P2CO2Hellmann
-
- P2CO2Hellmann.P2CO2SC - Class in etomica.models.co2
-
- P2CO2Hellmann.Parameters - Enum in etomica.models.co2
-
- P2CO2SC(double) - Constructor for class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- P2CO2TraPPE - Class in etomica.potential
-
I used this original EPM2model to describe TraPPECO2 model
the two models are different in parameters.
- P2CO2TraPPE(ISpace) - Constructor for class etomica.potential.P2CO2TraPPE
-
- P2Cohesion - Class in etomica.modules.droplet
-
Cohesive potential for mesoscale droplet simulation
- P2Cohesion(ISpace) - Constructor for class etomica.modules.droplet.P2Cohesion
-
- P2DiscreteFeynmanHibbs - Class in etomica.potential
-
Effective 2 body potential approximating the quantum behavior of atomic
interactions.
- P2DiscreteFeynmanHibbs(ISpace, Potential2Spherical) - Constructor for class etomica.potential.P2DiscreteFeynmanHibbs
-
- P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum - Class in etomica.potential
-
- P2DLPOLY - Class in etomica.potential
-
- P2DLPOLY(ISpace) - Constructor for class etomica.potential.P2DLPOLY
-
- P2DoubleWell - Class in etomica.potential
-
Double-well potential.
- P2DoubleWell(ISpace) - Constructor for class etomica.potential.P2DoubleWell
-
- P2DoubleWell(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2DoubleWell
-
- P2Dreiding - Class in etomica.potential
-
Dreiding potential.
- P2Dreiding(ISpace, double, double) - Constructor for class etomica.potential.P2Dreiding
-
- P2EffectiveFeynmanHibbs - Class in etomica.potential
-
Effective 2 body potential approximating the quantum behavior of atomic
interactions.
- P2EffectiveFeynmanHibbs(ISpace, Potential2SoftSpherical) - Constructor for class etomica.potential.P2EffectiveFeynmanHibbs
-
- P2Electrostatic - Class in etomica.potential
-
Simple electrostatic potential class.
- P2Electrostatic(ISpace) - Constructor for class etomica.potential.P2Electrostatic
-
- P2ElectrostaticDreiding - Class in etomica.paracetamol
-
Empirical Isotropic atom-atom repulsion-dispersion potential
Given formula:
U(r) = A*exp(-r/B) - C /r^6
A is in eV
B is in angstrom
C is in eV.angstrom^6
- P2ElectrostaticDreiding(ISpace) - Constructor for class etomica.paracetamol.P2ElectrostaticDreiding
-
- P2ElectrostaticDreiding(ISpace, double, double, double) - Constructor for class etomica.paracetamol.P2ElectrostaticDreiding
-
- P2ElectrostaticWithHardCore - Class in etomica.potential
-
Simple electrostatic potential class.
- P2ElectrostaticWithHardCore(ISpace) - Constructor for class etomica.potential.P2ElectrostaticWithHardCore
-
- P2EwaldReal() - Constructor for class etomica.potential.EwaldSummation.P2EwaldReal
-
- P2Exp6 - Class in etomica.potential
-
Exponential-6 atom-atom repulsion-dispersion potential.
- P2Exp6(ISpace) - Constructor for class etomica.potential.P2Exp6
-
- P2Exp6(ISpace, double, double, double) - Constructor for class etomica.potential.P2Exp6
-
- P2Exp6Buckingham - Class in etomica.potential
-
The Buckingham Exponential-6 atom-atom dispersion potential.
- P2Exp6Buckingham(ISpace) - Constructor for class etomica.potential.P2Exp6Buckingham
-
- P2Exp6Buckingham(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2Exp6Buckingham
-
- P2Fene - Class in etomica.potential
-
Finite elastic nonlinear extensible (FENE) spring potential.
- P2Fene(ISpace) - Constructor for class etomica.potential.P2Fene
-
- P2Fene(ISpace, double, double) - Constructor for class etomica.potential.P2Fene
-
- P2H2OSC(double) - Constructor for class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- P2HardAssociation - Class in etomica.potential
-
Purely attractive square-well potential with no repulsive core.
- P2HardAssociation(ISpace) - Constructor for class etomica.potential.P2HardAssociation
-
- P2HardAssociation(ISpace, double, double) - Constructor for class etomica.potential.P2HardAssociation
-
- P2HardAssociationCone - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationCone(ISpace) - Constructor for class etomica.potential.P2HardAssociationCone
-
- P2HardAssociationCone(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationCone
-
- P2HardAssociationConeDoubleSites - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationConeDoubleSites(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeDoubleSites
-
- P2HardAssociationConeFourSites - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationConeFourSites(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeFourSites
-
- P2HardAssociationConeFourSitesSW - Class in etomica.potential
-
Square-Well cone of attraction for associating fluid theory
Four association sites
- P2HardAssociationConeFourSitesSW(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeFourSitesSW
-
- P2HardAssociationConeOneSite - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationConeOneSite(ISpace) - Constructor for class etomica.potential.P2HardAssociationConeOneSite
-
- P2HardAssociationConeOneSite(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeOneSite
-
- P2HardAssociationConeReference - Class in etomica.potential
-
potential with a square-well cone of attraction for reference system.
- P2HardAssociationConeReference(ISpace, double) - Constructor for class etomica.potential.P2HardAssociationConeReference
-
- P2HardAssociationConeReferenceFourSites - Class in etomica.potential
-
potential with a square-well cone of attraction for reference system.
- P2HardAssociationConeReferenceFourSites(ISpace, double) - Constructor for class etomica.potential.P2HardAssociationConeReferenceFourSites
-
- P2HardAssociationConeSW - Class in etomica.potential
-
Square-Well cone of attraction for associating fluid theory
double association sites
- P2HardAssociationConeSW(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeSW
-
- P2HardAssociationGCPMReference - Class in etomica.models.water
-
- P2HardAssociationGCPMReference(ISpace, boolean) - Constructor for class etomica.models.water.P2HardAssociationGCPMReference
-
- P2HardAssociationRefAceticAcidTwoSite - Class in etomica.models.OPLS
-
- P2HardAssociationRefAceticAcidTwoSite() - Constructor for class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- P2HardBond - Class in etomica.potential
-
Potential that acts like a hard string connecting the centers of two atoms.
- P2HardBond(ISpace) - Constructor for class etomica.potential.P2HardBond
-
- P2HardBond(ISpace, double, double, boolean) - Constructor for class etomica.potential.P2HardBond
-
- P2HardBondedList - Class in etomica.potential
-
Hard potential that wraps two others.
- P2HardBondedList(Simulation, PotentialHard, PotentialHard) - Constructor for class etomica.potential.P2HardBondedList
-
- P2HardBondedList.BondArrayList - Class in etomica.potential
-
- P2HardSphere - Class in etomica.potential
-
Basic hard-(rod/disk/sphere) potential.
- P2HardSphere(ISpace) - Constructor for class etomica.potential.P2HardSphere
-
- P2HardSphere(ISpace, double, boolean) - Constructor for class etomica.potential.P2HardSphere
-
- P2HardSphereMC - Class in etomica.modules.colloid
-
- P2HardSphereMC(ISpace, AtomLeafAgentManager<? extends IAtomList>) - Constructor for class etomica.modules.colloid.P2HardSphereMC
-
- P2HardWrapper - Class in etomica.potential
-
Hard potential class that wraps another hard potential.
- P2HardWrapper(ISpace, PotentialHard) - Constructor for class etomica.potential.P2HardWrapper
-
- P2Harmonic - Class in etomica.potential
-
Harmonic Well interatomic potential.
- P2Harmonic(ISpace, double) - Constructor for class etomica.potential.P2Harmonic
-
- P2Harmonic(ISpace, double, double) - Constructor for class etomica.potential.P2Harmonic
-
- P2HC2Yukawa - Class in etomica.yukawa
-
Hard-core plus two Yukawa fluid (HC2Yukawa): A Lennard-Jones like potential.
- P2HC2Yukawa(ISpace) - Constructor for class etomica.yukawa.P2HC2Yukawa
-
- P2HC2Yukawa(ISpace, double, double) - Constructor for class etomica.yukawa.P2HC2Yukawa
-
- p2Head - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2HeadHead - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2HeadTail - Variable in class etomica.modules.interfacial.InterfacialSW
-
- P2HeEmpericalQuantum(ISpace, P2HePCKLJS, double) - Constructor for class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
-
- P2HePCKLJS - Class in etomica.potential
-
Ab initio pair potential for helium from Przybytek et al.
- P2HePCKLJS(ISpace) - Constructor for class etomica.potential.P2HePCKLJS
-
- P2HePCKLJS(ISpace, double) - Constructor for class etomica.potential.P2HePCKLJS
-
- P2HePCKLJS.P2HeQFH - Class in etomica.potential
-
This inner class can calculates the Feynman-Hibbs semiclassical
approximation for the potential.
- P2HePCKLJS.P2HeTI - Class in etomica.potential
-
- P2HeQFH(double) - Constructor for class etomica.potential.P2HePCKLJS.P2HeQFH
-
- P2HeQFH(double) - Constructor for class etomica.potential.P2HeSimplified.P2HeQFH
-
- P2HeSimplified - Class in etomica.potential
-
Simplified pair potential for Helium.
- P2HeSimplified(ISpace) - Constructor for class etomica.potential.P2HeSimplified
-
- P2HeSimplified.P2HeQFH - Class in etomica.potential
-
This inner class can calculates the Feynman-Hibbs semiclassical
approximation for the potential.
- P2HeSimplified.P2HeTI - Class in etomica.potential
-
- P2HeTI(double) - Constructor for class etomica.potential.P2HePCKLJS.P2HeTI
-
- P2HeTI(double) - Constructor for class etomica.potential.P2HeSimplified.P2HeTI
-
- p2Hinde - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- p2Hinde - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- P2HSDipole - Class in etomica.potential
-
Hard sphere molecule with a dipole sitting at the center.
- P2HSDipole(ISpace) - Constructor for class etomica.potential.P2HSDipole
-
- P2HSDipole(ISpace, double) - Constructor for class etomica.potential.P2HSDipole
-
- P2HSDipole(ISpace, double, double) - Constructor for class etomica.potential.P2HSDipole
-
- P2HSDipole(ISpace, double, double, double) - Constructor for class etomica.potential.P2HSDipole
-
- P2HydrogenHinde - Class in etomica.potential
-
- P2HydrogenHinde(ISpace) - Constructor for class etomica.potential.P2HydrogenHinde
-
- P2HydrogenHinde.P2HydrogenHindeAtomic - Class in etomica.potential
-
- P2HydrogenHinde.P2HydrogenHindeMolecular - Class in etomica.potential
-
- P2HydrogenHindeAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHinde.P2HydrogenHindeAtomic
-
- P2HydrogenHindeAtomic - Class in etomica.potential
-
- P2HydrogenHindeAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHindeAtomic
-
- P2HydrogenHindeMolecular(ISpace) - Constructor for class etomica.potential.P2HydrogenHinde.P2HydrogenHindeMolecular
-
- P2HydrogenHindePatkowski - Class in etomica.potential
-
- P2HydrogenHindePatkowski(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowski
-
- P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular - Class in etomica.potential
-
- P2HydrogenHindePatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic
-
- P2HydrogenHindePatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenHindePatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- P2HydrogenHindePatkowskiMolecular(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular
-
- P2HydrogenMielkeAtomic(ISpace) - Constructor for class etomica.potential.P1HydrogenMielke.P2HydrogenMielkeAtomic
-
- P2HydrogenPatkowski - Class in etomica.potential
-
- P2HydrogenPatkowski(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowski
-
- P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular - Class in etomica.potential
-
- P2HydrogenPatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic
-
- P2HydrogenPatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenPatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowskiAtomic
-
- P2HydrogenPatkowskiIso - Class in etomica.potential
-
- P2HydrogenPatkowskiIso(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowskiIso
-
- P2HydrogenPatkowskiMolecular(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular
-
- P2Ideal - Class in etomica.potential
-
Ideal-gas two-body potential, which defines no interactions and zero energy
for all pairs given to it.
- P2Ideal(ISpace) - Constructor for class etomica.potential.P2Ideal
-
- P2LennardJones - Class in etomica.potential
-
Lennard-Jones interatomic potential.
- P2LennardJones(ISpace) - Constructor for class etomica.potential.P2LennardJones
-
- P2LennardJones(ISpace, double, double) - Constructor for class etomica.potential.P2LennardJones
-
- P2LennardJonesDreiding - Class in etomica.potential
-
Dreiding: Lennard-Jones non-bonding potential.
- P2LennardJonesDreiding(ISpace) - Constructor for class etomica.potential.P2LennardJonesDreiding
-
- P2LennardJonesDreiding(ISpace, double, double) - Constructor for class etomica.potential.P2LennardJonesDreiding
-
- p2LJ - Variable in class etomica.modules.droplet.DropletAtomic
-
- p2LJ - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- p2LJ - Variable in class etomica.normalmode.SimLJVacancy
-
- p2lj - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- p2lj - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- P2LJDipole - Class in etomica.potential
-
Lennard Jones molecule with a point dipole sitting in the center.
- P2LJDipole(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2LJDipole
-
- P2LJDipole - Class in etomica.rotation
-
r^-12 potential plus a point dipole, force shifted, as used in
Kol, Laird and Leimkuhler, JCP 107 (1997) 2580-2588.
- P2LJDipole(ISpace) - Constructor for class etomica.rotation.P2LJDipole
-
- P2LJDipole(ISpace, double, double, double) - Constructor for class etomica.rotation.P2LJDipole
-
- p2LJQ - Variable in class etomica.modules.vle.VLESim
-
- P2LJQ - Class in etomica.potential
-
Lennard Jones molecule with a quadrupole.
- P2LJQ(ISpace) - Constructor for class etomica.potential.P2LJQ
-
- P2LJQ(ISpace, double, double, double) - Constructor for class etomica.potential.P2LJQ
-
- P2LJQQ - Class in etomica.potential
-
Lennard Jones molecule with a quadrupole.
- P2LJQQ(ISpace) - Constructor for class etomica.potential.P2LJQQ
-
- P2LJQQ(ISpace, double, double, double) - Constructor for class etomica.potential.P2LJQQ
-
- p2LJt - Variable in class etomica.modules.droplet.DropletAtomic
-
- p2mc - Variable in class etomica.modules.colloid.ColloidSim
-
- p2mc - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- p2mm - Variable in class etomica.modules.colloid.ColloidSim
-
- P2ModifiedMorse - Class in etomica.potential
-
- P2ModifiedMorse(ISpace) - Constructor for class etomica.potential.P2ModifiedMorse
-
- P2ModifiedMorse(ISpace, double, double, double, double, double, double) - Constructor for class etomica.potential.P2ModifiedMorse
-
- P2MoleculeMonatomic - Class in etomica.potential
-
- P2MoleculeMonatomic(IPotentialAtomic) - Constructor for class etomica.potential.P2MoleculeMonatomic
-
- P2MoleculeSoftTruncatedSwitched - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2MoleculeSoftTruncatedSwitched(IPotentialMolecularTorque, double, ISpace) - Constructor for class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- P2MoleculeTruncated - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2MoleculeTruncated(IPotentialMolecular, double, ISpace, IAtomPositionDefinition) - Constructor for class etomica.potential.P2MoleculeTruncated
-
- P2Morse - Class in etomica.potential
-
- P2Morse(ISpace) - Constructor for class etomica.potential.P2Morse
-
- P2Morse(ISpace, double, double, double) - Constructor for class etomica.potential.P2Morse
-
- p2N2HellmannA - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- P2N2QFH(double) - Constructor for class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- P2Nitrogen - Class in etomica.models.nitrogen
-
P2 6-point potential for Nitrogen.
- P2Nitrogen(ISpace, double) - Constructor for class etomica.models.nitrogen.P2Nitrogen
-
- P2NitrogenAB - Class in etomica.models.nitrogen
-
P2 6-point potential for Nitrogen.
- P2NitrogenAB(ISpace, double) - Constructor for class etomica.models.nitrogen.P2NitrogenAB
-
- P2NitrogenAnisotropic - Class in etomica.models.nitrogen
-
P2 6-point potential for Nitrogen with anisotropic contribution
Reference: 1.
- P2NitrogenAnisotropic(ISpace, double) - Constructor for class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- P2NitrogenHellmann - Class in etomica.potential
-
- P2NitrogenHellmann(ISpace) - Constructor for class etomica.potential.P2NitrogenHellmann
-
- P2NitrogenHellmann.P2N2QFH - Class in etomica.potential
-
- P2NitrogenShellModel - Class in etomica.models.nitrogen
-
CAUTION!!!!!! The potential DOES NOT really describe the ALPHA and GAMMA structure at
NON-ZERO temperature condition!!
(through observation [SimulationGraphic]
and pressure calculation[MeterPressureMolecular])
P2 shell-model potential for Nitrogen.
- P2NitrogenShellModel(ISpace, double) - Constructor for class etomica.models.nitrogen.P2NitrogenShellModel
-
- P2O2Bartolomei - Class in etomica.potential
-
- P2O2Bartolomei(ISpace) - Constructor for class etomica.potential.P2O2Bartolomei
-
- P2O2Bartolomei.P2O2TI - Class in etomica.potential
-
- P2O2TI(double) - Constructor for class etomica.potential.P2O2Bartolomei.P2O2TI
-
- p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- p2Patkowski - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- p2Patkowski - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- P2PenetrableBond - Class in etomica.potential
-
Potential with a well having a finite potential on either side.
- P2PenetrableBond(ISpace) - Constructor for class etomica.potential.P2PenetrableBond
-
- P2PenetrableBond(ISpace, double, double, boolean) - Constructor for class etomica.potential.P2PenetrableBond
-
- P2PenetrableCar(ISpace, ParseObj, IBox) - Constructor for class etomica.modules.render.RenderMD.P2PenetrableCar
-
- P2PenetrableSphere - Class in etomica.potential
-
Basic penetrable-sphere potential.
- P2PenetrableSphere(ISpace) - Constructor for class etomica.potential.P2PenetrableSphere
-
Constructor with default values of unity for core diameter and core energy.
- P2PenetrableSphere(ISpace, double, double) - Constructor for class etomica.potential.P2PenetrableSphere
-
- P2PenetrableSquareWell - Class in etomica.potential
-
Square-well potential with a penetrable core.
- P2PenetrableSquareWell(ISpace) - Constructor for class etomica.potential.P2PenetrableSquareWell
-
- P2PenetrableSquareWell(ISpace, double, double, double, boolean) - Constructor for class etomica.potential.P2PenetrableSquareWell
-
- p2pseudo - Variable in class etomica.modules.colloid.ColloidSim
-
- p2pseudo - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- P2QChem - Class in etomica.potential
-
This class requires a bash script called ./runQChem to load the appropriate Q-Chem module and run it.
- P2QChem(ISpace) - Constructor for class etomica.potential.P2QChem
-
- P2QChemInterpolated - Class in etomica.potential
-
Pair potential for argon interpolated from Q-Chem results.
- P2QChemInterpolated(ISpace) - Constructor for class etomica.potential.P2QChemInterpolated
-
- P2QChemInterpolated.DampingParams - Class in etomica.potential
-
- P2ReactionFieldDipole - Class in etomica.potential
-
- P2ReactionFieldDipole(ISpace, IAtomPositionDefinition) - Constructor for class etomica.potential.P2ReactionFieldDipole
-
- P2ReactionFieldDipole.P0ReactionField - Class in etomica.potential
-
A 0-body potential that should be added along with this potential.
- P2ReactionFieldDipoleTruncated - Class in etomica.potential
-
- P2ReactionFieldDipoleTruncated(ISpace, IAtomPositionDefinition) - Constructor for class etomica.potential.P2ReactionFieldDipoleTruncated
-
- P2ReactionFieldDipoleTruncated.P0ReactionField - Class in etomica.potential
-
A 0-body potential that should be added along with this potential.
- P2RepRowley - Class in etomica.models.rowley
-
Purely repulsive potential from Rowley et al (2006) used for interactions between satellite sites, X.
- P2RepRowley(ISpace) - Constructor for class etomica.models.rowley.P2RepRowley
-
- P2RepRowley(ISpace, double, double) - Constructor for class etomica.models.rowley.P2RepRowley
-
- P2RoughSphere - Class in etomica.potential
-
Basic hard-(rod/disk/sphere) potential, with surface roughness to couple rotation and translational motions.
- P2RoughSphere(ISpace) - Constructor for class etomica.potential.P2RoughSphere
-
- P2RoughSphere(ISpace, double, boolean) - Constructor for class etomica.potential.P2RoughSphere
-
- p2S - Variable in class etomica.modules.sam.Sam
-
- p2SCH2 - Variable in class etomica.modules.sam.Sam
-
- p2SCH2t - Variable in class etomica.modules.sam.Sam
-
- P2SemiclassicalAtomic - Class in etomica.potential
-
Effective semiclassical molecular potential using the approach of
Takahashi and Imada
http://dx.doi.org/10.1143/JPSJ.53.3765
as described by Schenter
http://dx.doi.org/10.1063/1.1505441
- P2SemiclassicalAtomic(ISpace, IPotentialTorque, double) - Constructor for class etomica.potential.P2SemiclassicalAtomic
-
- P2SemiclassicalAtomic.AtomInfo - Interface in etomica.potential
-
- P2SemiclassicalMolecular - Class in etomica.potential
-
Effective semiclassical molecular potential using the approach of
Takahashi and Imada
http://dx.doi.org/10.1143/JPSJ.53.3765
as described by Schenter
http://dx.doi.org/10.1063/1.1505441
- P2SemiclassicalMolecular(ISpace, IPotentialMolecularTorque) - Constructor for class etomica.potential.P2SemiclassicalMolecular
-
- P2SemiclassicalMolecular.MoleculeInfo - Interface in etomica.potential
-
- P2SemiclassicalMolecular.MoleculeInfoBrute - Class in etomica.potential
-
- p2Soft - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- p2Soft - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- p2Soft - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- P2SoftSphere - Class in etomica.potential
-
Soft-sphere interatomic potential.
- P2SoftSphere(ISpace) - Constructor for class etomica.potential.P2SoftSphere
-
- P2SoftSphere(ISpace, double, double, int) - Constructor for class etomica.potential.P2SoftSphere
-
- P2SoftSphericalTruncated - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftSphericalTruncated(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncated
-
- P2SoftSphericalTruncated.P0Lrc - Class in etomica.potential
-
Inner class that implements the long-range correction for this truncation scheme.
- P2SoftSphericalTruncatedForceShifted - Class in etomica.potential
-
Soft-spherical potential class that shifts both the potential energy and the
force such that both are 0 at the cutoff.
- P2SoftSphericalTruncatedForceShifted(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedForceShifted
-
- P2SoftSphericalTruncatedShifted - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftSphericalTruncatedShifted(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedShifted
-
- P2SoftSphericalTruncatedSwitched - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftSphericalTruncatedSwitched(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- P2SoftTruncated - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftTruncated(Potential2Soft, double, ISpace) - Constructor for class etomica.potential.P2SoftTruncated
-
- P2SpheroPolyhedron - Class in etomica.potential
-
- P2SpheroPolyhedron(ISpace) - Constructor for class etomica.potential.P2SpheroPolyhedron
-
- P2Spin - Class in etomica.spin
-
Magnetic spin potential, with an energy defined by
U = -J r1 dot r2
where J is a coupling parameter, and r1 and r2 are the vectors given by
atom.coord.position.
- P2Spin(ISpace) - Constructor for class etomica.spin.P2Spin
-
- P2Spin(ISpace, double) - Constructor for class etomica.spin.P2Spin
-
- P2SquareWell - Class in etomica.potential
-
Basic square-well potential.
- P2SquareWell(ISpace) - Constructor for class etomica.potential.P2SquareWell
-
- P2SquareWell(ISpace, double, double, double, boolean) - Constructor for class etomica.potential.P2SquareWell
-
- P2SquareWellBonded - Class in etomica.modules.chainequilibrium
-
Similar to square-well potential, but considers and alters bonding states
with collisions.
- P2SquareWellBonded(ISpace, AtomLeafAgentManager, double, double, double) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- P2SquareWellBonded - Class in etomica.modules.reactionequilibrium
-
Similar to square-well potential, but considers and alters bonding states
with collisions.
- P2SquareWellBonded(ISpace, AtomLeafAgentManager, double, double, double, boolean) - Constructor for class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- P2SquareWellBonded.RingResult - Class in etomica.modules.chainequilibrium
-
- P2SquareWellBonding - Class in etomica.modules.catalysis
-
Basic square-well potential.
- P2SquareWellBonding(ISpace, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBonding
-
- P2SquareWellBondingCO - Class in etomica.modules.catalysis
-
Basic square-well potential.
- P2SquareWellBondingCO(ISpace, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBondingCO
-
- P2SquareWellMonomer - Class in etomica.modules.colloid
-
- P2SquareWellMonomer(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P2SquareWellMonomer
-
- P2SquareWellOneSide - Class in etomica.modules.mu
-
Basic square-well potential.
- P2SquareWellOneSide(ISpace) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
-
- P2SquareWellOneSide(ISpace, double, double, double, boolean) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
-
- P2SquareWellRadical - Class in etomica.modules.chainequilibrium
-
Similar to square-well potential, but considers and alters bonding states
with collisions based on free radical reactions.
- P2SquareWellRadical(ISpace, AtomLeafAgentManager, double, double, double, IRandom) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- P2SquareWellRobust - Class in etomica.potential
-
Basic square-well potential.
- P2SquareWellRobust(ISpace) - Constructor for class etomica.potential.P2SquareWellRobust
-
- P2SquareWellRobust(ISpace, double, double, double, boolean) - Constructor for class etomica.potential.P2SquareWellRobust
-
- P2SquareWellSurface - Class in etomica.modules.catalysis
-
Basic square-well potential.
- P2SquareWellSurface(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
-
- P2SquareWellSurface(ISpace, AtomLeafAgentManager, double, double, double, int) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
-
- p2St - Variable in class etomica.modules.sam.Sam
-
- p2SulfurSurfaceLJ - Variable in class etomica.modules.sam.Sam
-
- p2SurfaceBond - Variable in class etomica.modules.sam.Sam
-
- p2Tail - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2TailTail - Variable in class etomica.modules.interfacial.InterfacialSW
-
- P2Tether - Class in etomica.potential
-
Potential that acts like a hard string connecting the centers of two atoms.
- P2Tether(ISpace) - Constructor for class etomica.potential.P2Tether
-
- P2Tether(ISpace, double, boolean) - Constructor for class etomica.potential.P2Tether
-
- P2TriangleWell - Class in etomica.potential
-
Hard core with an attractive tail that goes to zero linearly with r.
- P2TriangleWell(ISpace) - Constructor for class etomica.potential.P2TriangleWell
-
- P2TriangleWell(ISpace, double, double, double) - Constructor for class etomica.potential.P2TriangleWell
-
- p2Truncated - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- p2Truncated - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- p2Truncated - Variable in class etomica.modules.vle.VLESim
-
- p2TruncatedShifted - Variable in class etomica.mappedvirial.MappedU
-
- P2Water3P - Class in etomica.models.water
-
3-point potential for water.
- P2Water3P(ISpace, double, double, double, double) - Constructor for class etomica.models.water.P2Water3P
-
- P2Water3PSoft - Class in etomica.models.water
-
3-point potential for water that can calculate gradient and torque (for the
center of mass of the water molecule).
- P2Water3PSoft(ISpace, double, double, double, double) - Constructor for class etomica.models.water.P2Water3PSoft
-
- P2Water4P - Class in etomica.models.water
-
4-point potential for water.
- P2Water4P(ISpace, double, double, double, double, IAtomPositionDefinition) - Constructor for class etomica.models.water.P2Water4P
-
- P2Water4PSoft - Class in etomica.models.water
-
3-point potential for water that can calculate gradient and torque (for the
center of mass of the water molecule).
- P2Water4PSoft(ISpace, double, double, double, double, IAtomPositionDefinition) - Constructor for class etomica.models.water.P2Water4PSoft
-
- P2Water4PSoft.AtomicTensorAtomicPair - Interface in etomica.models.water
-
- P2WaterPotentialsJankowski - Class in etomica.potential
-
- P2WaterPotentialsJankowski(ISpace, int, int, double, IPotentialAtomic) - Constructor for class etomica.potential.P2WaterPotentialsJankowski
-
- P2WaterSPC - Class in etomica.models.water
-
SPC potential for water.
- P2WaterSPC(ISpace) - Constructor for class etomica.models.water.P2WaterSPC
-
- P2WaterSPCE - Class in etomica.models.water
-
SPC/E potential for water.
- P2WaterSPCE(ISpace) - Constructor for class etomica.models.water.P2WaterSPCE
-
- P2WaterSPCSoft - Class in etomica.models.water
-
SPC potential for water.
- P2WaterSPCSoft(ISpace) - Constructor for class etomica.models.water.P2WaterSPCSoft
-
- P2WaterSzalewicz - Class in etomica.models.water
-
Water potential as described by
http://dx.doi.org/10.1063/1.4875097
This class handles 2-body, 3-body and induction terms.
- P2WaterSzalewicz(ISpace, int) - Constructor for class etomica.models.water.P2WaterSzalewicz
-
- P2WaterSzalewicz.Component - Enum in etomica.models.water
-
- P2WaterSzalewicz.P2H2OSC - Class in etomica.models.water
-
- P2WaterTIP4P - Class in etomica.models.water
-
TIP4P potential for water.
- P2WaterTIP4P(ISpace) - Constructor for class etomica.models.water.P2WaterTIP4P
-
- P2WaterTIP4P(ISpace, double) - Constructor for class etomica.models.water.P2WaterTIP4P
-
- P2WaterTIP4PHardCore - Class in etomica.models.water
-
4-point potential for water.
- P2WaterTIP4PHardCore(ISpace, double, double, double, double, double) - Constructor for class etomica.models.water.P2WaterTIP4PHardCore
-
- P2WaterTIP4PSoft - Class in etomica.models.water
-
TIP4P potential for water.
- P2WaterTIP4PSoft(ISpace, double, IAtomPositionDefinition) - Constructor for class etomica.models.water.P2WaterTIP4PSoft
-
- P2WCA - Class in etomica.potential
-
Weeks-Chandler-Andersen potential.
- P2WCA(ISpace) - Constructor for class etomica.potential.P2WCA
-
Constructs potential using default sigma and epsilon given by Default class.
- P2WCA(ISpace, double, double) - Constructor for class etomica.potential.P2WCA
-
- P2XOrder - Class in etomica.normalmode
-
Hard potential that enforces ordering of the x-coordinates of the
pairs.
- P2XOrder(ISpace, Potential2HardSpherical) - Constructor for class etomica.normalmode.P2XOrder
-
- P2Yukawa - Class in etomica.yukawa
-
Yukawa interatomic potential.
- P2Yukawa(ISpace) - Constructor for class etomica.yukawa.P2Yukawa
-
- P2Yukawa(ISpace, double, double) - Constructor for class etomica.yukawa.P2Yukawa
-
- p3 - Variable in class etomica.virial.MayerFunctionMolecularThreeBody
-
- p3 - Variable in class etomica.virial.MayerFunctionSphericalThreeBody
-
- P3AdditiveQChem - Class in etomica.potential
-
- P3AdditiveQChem() - Constructor for class etomica.potential.P3AdditiveQChem
-
- P3AdditiveQChem.DampingParams - Class in etomica.potential
-
- P3AxilrodTeller - Class in etomica.potential
-
Axilrod-Teller potential.
- P3AxilrodTeller(ISpace, AtomTypeAgentManager) - Constructor for class etomica.potential.P3AxilrodTeller
-
- P3AxilrodTeller.MyAgent - Class in etomica.potential
-
- p3Bond - Variable in class etomica.modules.sam.Sam
-
- P3BondAngle - Class in etomica.potential
-
Simple 3-body soft bond-angle potential
- P3BondAngle(ISpace) - Constructor for class etomica.potential.P3BondAngle
-
- P3BondAngleDreiding - Class in etomica.potential
-
Simple 3-body soft bond-angle for Dreiding potential
* U(theta) = gamma * [ cos(theta) - cos(theta_e)]^2
where gamma is the potential's energy parameter
theta_e is the equilibrium bond angle
- P3BondAngleDreiding(ISpace, double, double) - Constructor for class etomica.potential.P3BondAngleDreiding
-
- P3CPSNonAdditiveHe - Class in etomica.potential
-
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHe(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHe
-
- P3CPSNonAdditiveHeLessSimplified - Class in etomica.potential
-
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHeLessSimplified(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- P3CPSNonAdditiveHeOrig - Class in etomica.potential
-
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHeOrig(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHeOrig
-
- P3CPSNonAdditiveHeSimplified - Class in etomica.potential
-
Simplified version of ab initio, non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHeSimplified(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- P3GCPMAxilrodTeller(ISpace) - Constructor for class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- P3GCPMAxilrodTeller(ISpace) - Constructor for class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- P3HydrogenATM - Class in etomica.potential
-
- P3HydrogenATM(ISpace) - Constructor for class etomica.potential.P3HydrogenATM
-
- P3HydrogenATM.P3HydrogenAtomic - Class in etomica.potential
-
- P3HydrogenAtomic(ISpace) - Constructor for class etomica.potential.P3HydrogenATM.P3HydrogenAtomic
-
- P3HydrogenGarberoglioMolecular - Class in etomica.potential
-
- P3HydrogenGarberoglioMolecular(ISpace) - Constructor for class etomica.potential.P3HydrogenGarberoglioMolecular
-
- P3HydrogenManzhos - Class in etomica.potential
-
- P3HydrogenManzhos(ISpace) - Constructor for class etomica.potential.P3HydrogenManzhos
-
- P3HydrogenManzhos.P3HydrogenManzhosMolecular - Class in etomica.potential
-
- P3HydrogenManzhosMolecular(ISpace) - Constructor for class etomica.potential.P3HydrogenManzhos.P3HydrogenManzhosMolecular
-
- P3Induction - Class in etomica.potential
-
3-body induction potential based on form used by Oakley and Wheatley.
- P3Induction(ISpace, AtomTypeAgentManager) - Constructor for class etomica.potential.P3Induction
-
- P3Induction.MyAgent - Class in etomica.potential
-
- p3N2HellmannA - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- p3N2HellmannA - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- P3NitrogenHellmannNonAdditive - Class in etomica.potential
-
- P3NitrogenHellmannNonAdditive(ISpace) - Constructor for class etomica.potential.P3NitrogenHellmannNonAdditive
-
- p3ParametersFile - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- P3QChem - Class in etomica.potential
-
- P3QChem() - Constructor for class etomica.potential.P3QChem
-
- P3QChem.DampingParams - Class in etomica.potential
-
- p4BondCCCC - Variable in class etomica.modules.sam.Sam
-
- p4BondCCCS - Variable in class etomica.modules.sam.Sam
-
- P4BondTorsion - Class in etomica.potential
-
Torsion potential.
- P4BondTorsion(ISpace, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsion
-
- P4BondTorsionAlkaneXCCH - Class in etomica.potential
-
slight modification from P4BondTorsion class(change energyAtAngle method)
Siepmann's Alkane TraPPE-EH model, XCCH torsion potential, X can be H or C, H is for H on CH3 only
U(torsion) = Cx * (1 -cos(3phi)); C(C):854K, C(H):717K
- P4BondTorsionAlkaneXCCH(ISpace, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsionAlkaneXCCH
-
- P4BondTorsionOPLS - Class in etomica.potential
-
OPLS Torsion potential.
- P4BondTorsionOPLS(ISpace, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsionOPLS
-
- P4TorsionDreiding - Class in etomica.potential
-
Simple 4-body soft bond-angle for Dreiding potential
U(phi) = (1/2) * Vjk * {1 - cos [njk (phi - phiEq)]}
where Vjk is the rotation barrier (always +ve) [unit Kelvin]
njk is the periodicity (an integer)
phiEq is the equilibrium dihedral angle [unit radians]
- P4TorsionDreiding(ISpace, double, double, int) - Constructor for class etomica.potential.P4TorsionDreiding
-
- pac - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- PadeApproximation - Class in etomica.util.numerical
-
Class to approximate a power series with rational function (Pade Approximation)
Pade[K/L] = A_K/ C_L = B_M
with Kth, Lth and Mth order, where K + L = M
a0 + a1*x + a2*x^2 + ...
- PadeApproximation(double[], int, int) - Constructor for class etomica.util.numerical.PadeApproximation
-
- PadeApproximation.VirialParam - Class in etomica.util.numerical
-
- paint(Graphics) - Method in class etomica.graphics.AboutBoxWindow
-
- paint(Graphics) - Method in class etomica.graphics.DisplayCanvas
-
- paint(Graphics) - Method in class etomica.graphics.DisplayScrollingGraph
-
- paint() - Method in class etomica.modules.clustergenerator.ClusterPanel
-
- paint() - Method in class etomica.modules.clustergenerator.Plot
-
Classes which inherit from Plot must define this method.
- paint(Graphics) - Method in class etomica.modules.clustergenerator.Plot
-
- paint(Graphics) - Method in class etomica.util.Grabber.ImagePanel
-
- paintComponent(Graphics) - Method in class etomica.graphics.EtomicaPlot
-
- pair - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- pair - Variable in class etomica.association.BiasVolumeAceticAcid
-
- pair - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- pair - Variable in class etomica.atom.iterator.ApiIndexList
-
- pair - Variable in class etomica.atom.iterator.ApiInnerVariable
-
- pair - Variable in class etomica.atom.iterator.ApiIntergroup
-
- pair - Variable in class etomica.atom.iterator.MpiInnerVariable
-
- pair - Variable in class etomica.mappedvirial.MappedUpotential
-
- pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- pair - Variable in class etomica.models.co2.PNCO2GCPM
-
- pair - Variable in class etomica.models.co2.PNGCPM
-
- pair - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- pair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- pair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- pair - Variable in class etomica.models.water.PNWaterGCPM
-
- pair - Variable in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
-
- pair - Variable in class etomica.nbr.list.NeighborListManagerSlanty
-
- pair - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- pair - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- pair - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- pair - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- pair - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- pair - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- pair - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- pairAB - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- pairAB - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- pairAB - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- pairAgents - Variable in class etomica.models.co2.PNGCPM
-
- pairDone - Variable in class etomica.virial.PotentialCommonAtomic
-
- pairDone - Variable in class etomica.virial.PotentialGroupPI
-
- pairForce(IAtom, IAtom) - Method in class etomica.models.water.P2Water4PSoft
-
- pairId(int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the pair ID for the given indices (id0, id1, id2)
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- pairOnly - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- pairOnly - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- pairOnly - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- pairOnly - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- pairPolarization - Variable in class etomica.models.co2.PNGCPM
-
- pairPotential - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- pairPotential - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- pairPotential - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- pairPotentialIndex - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- pairSum - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
-
- PALETTE_ALTLOC - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_AMINO - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_CHAIN - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_CPK - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_ENERGY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_FIXEDTEMP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_FORMAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_GROUP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_INSERTION - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_JMOL - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_MOLECULE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_MONOMER - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_NONE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_PARTIAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_POLYMER - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_PROPERTY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_RASMOL - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_SHAPELY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_STRAIGHTNESS - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_STRUCTURE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_SURFACE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_TEMP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_TYPE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_VARIABLE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_VOLATILE - Static variable in class org.jmol.constant.StaticConstants
-
- panel - Variable in class etomica.graphics.DeviceBox
-
Displayed panel that holds the label and value
(not yet used; meant to implement to make lightweight display)
- panel - Variable in class etomica.graphics.DisplayPlot
-
- panel - Variable in class etomica.graphics.DisplayTable
-
- panel - Variable in class etomica.graphics.DisplayTextBox
-
Displayed panel that holds the label and value
(not yet used; meant to implement to make lightweight display)
- panel - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- panel - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- PanelMainFrame - Class in etomica.virial.GUI.containers
-
- PanelMainFrame(int, int) - Constructor for class etomica.virial.GUI.containers.PanelMainFrame
-
- panelParentGroup - Variable in class etomica.graphics.DisplayTextBoxesCAE
-
- parab - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- Parallelepiped - Class in etomica.math.geometry
-
A polyhedron composed of three pairs of rectangular faces placed opposite
each other and joined at arbitrary angles.
- Parallelepiped(ISpace) - Constructor for class etomica.math.geometry.Parallelepiped
-
Default constructor makes a cube of unit size
- Parallelepiped(ISpace, IVector, IVector, IVector) - Constructor for class etomica.math.geometry.Parallelepiped
-
Constructs a parallelepiped with the given edge vectors.
- Parallelogram - Class in etomica.math.geometry
-
A quadrilateral with opposite sides parallel
.
- Parallelogram(ISpace) - Constructor for class etomica.math.geometry.Parallelogram
-
Default constructor makes a square of unit size
- Parallelogram(ISpace, IVector, IVector) - Constructor for class etomica.math.geometry.Parallelogram
-
Constructs a parallelogram with the given edge vectors.
- Parallelotope - Interface in etomica.math.geometry
-
Polytope having parallel faces, and which can be specified via a set of edge vectors.
- Param() - Constructor for class etomica.AlkaneEH.CH4NVT.Param
-
- Param() - Constructor for class etomica.AlkaneEH.DHS_NVT.Param
-
- Param() - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- Param() - Constructor for class etomica.dielectric.DHS_NVT.Param
-
- Param() - Constructor for class etomica.dielectric.DLJ_NVT_1site.Param
-
- Param() - Constructor for class etomica.dielectric.TIP4P_NVT.Param
-
- param - Variable in class etomica.modules.interfacial.FitTanh
-
- param - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- param - Variable in class etomica.surfacetension.FitTanh
-
- PARAM_ALL - Static variable in class etomica.graph.operations.MaxIsomorph
-
Parameters instance which does not filter out any graph property.
- PARAM_ROOTY - Static variable in class etomica.graph.operations.MaxIsomorph
-
- ParameterBase - Class in etomica.util
-
Base class for all parameter wrapper implementations.
- ParameterBase() - Constructor for class etomica.util.ParameterBase
-
- parameterGraphic() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the panel that contains the parameter sliders.
- ParameterParser - Interface in etomica.util
-
- Parameters - Interface in etomica.graph.operations
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- parametersB - Variable in class etomica.potential.P2NitrogenHellmann
-
- parametersB - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- ParameterSetMEAM - Class in etomica.meam
-
This class provides the MEAM parameters for the SAC alloy constituents
(Ag, Cu, and Sn) and for the reference structures required for cross
potentials (the pair potentials between atoms of different types).
- ParameterSetMEAM(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.meam.ParameterSetMEAM
-
- params - Variable in class etomica.graph.operations.UnaryChain.ChainParameters
-
- Params() - Constructor for class etomica.meam.EFSTungsten.Params
-
- params - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- Params() - Constructor for class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- params - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- params - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- params3 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- paramsManager - Variable in class etomica.potential.P3AxilrodTeller
-
- paramsManager - Variable in class etomica.potential.P3Induction
-
- parent - Variable in class etomica.atom.Atom
-
- parentColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
-
- parentGroup - Variable in class etomica.atom.iterator.ApiIndexList
-
- parentType - Variable in class etomica.atom.AtomTypeLeaf
-
- ParmedParser - Class in etomica.parser
-
Class that generates
ParmedStructure objects by invoking
the
ParmEd library and serializing its
Structure object using JSON.
- ParmedParser() - Constructor for class etomica.parser.ParmedParser
-
- ParmedStructure - Class in etomica.parser
-
Class that contains the data from a
ParmEd Structure,
and has methods to load this data into various
etomica components.
- parse(String) - Method in class etomica.graph.engine.impl.ParserImpl
-
- parse(String) - Method in interface etomica.graph.engine.Parser
-
- parse(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
Parse out a number from the given text and return it as a Long if
possible; otherwise, return it as a Double.
- parseARGB(String) - Method in class etomica.graph.view.rasterizer.Main.ColorOptionHandler
-
Parse the input value, which should be in the following
format: a.r.g.b where a, r, g and b are integer values,
in decimal notation, between 0 and 255.
- ParseArgs - Class in etomica.util
-
Class that handles parsing of commandline arguments.
- ParseArgs() - Constructor for class etomica.util.ParseArgs
-
- ParseArgs(ParameterBase) - Constructor for class etomica.util.ParseArgs
-
- parseArgs(String[]) - Method in class etomica.util.ParseArgs
-
Parses each argument and attempts to match it with a field from
parameterWrapper and sets the field to the value from the next argument.
- parseArgs(String[], boolean) - Method in class etomica.util.ParseArgs
-
- parseAsDecimal(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
parse the input string, interpreting it as regular decimal format.
- parseAsExponential(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
parse the input string, interpreting it as exponential format.
- parseAsFlexible(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
parse the input string, interpreting it as either regular decimal
format or exponential format.
- parseFloatArray(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArray2d(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArray3d(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArrayBsData(String[], BitSet, float[]) - Static method in class org.jmol.util.Parser
-
- parseFloatArrayData(String[], float[]) - Static method in class org.jmol.util.Parser
-
parses a string array for floats.
- parseFloatArrayDataN(String[], float[], int) - Static method in class org.jmol.util.Parser
-
parses a string array for floats.
- parseFloatArrayFromMatchAndField(String, BitSet, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
-
the major lifter here.
- parseFloatArrayNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseFloatNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseFloatRange(String, int, int[]) - Static method in class org.jmol.util.Parser
-
- parseFloatStr(String) - Static method in class org.jmol.util.Parser
-
- parseFloatStrict(String) - Static method in class org.jmol.util.Parser
-
- parseGromacs(File, File) - Static method in class etomica.parser.ParmedParser
-
Parses the given
Gromacs .top and .gro files
using the
ParmEd python library.
- parseGromacsResourceFiles(String, String) - Static method in class etomica.parser.ParmedParser
-
Convenience method to parse gromacs files located in the etomica-core/src/main/resources directory.
- parseInt(String) - Static method in class org.jmol.util.Parser
-
- parseIntNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseIntRadix(String, int) - Static method in class org.jmol.util.Parser
-
- parseIntRange(String, int, int[]) - Static method in class org.jmol.util.Parser
-
- ParseObj - Class in etomica.modules.render
-
- ParseObj(String) - Constructor for class etomica.modules.render.ParseObj
-
- ParseObj.BondInfo - Class in etomica.modules.render
-
- Parser - Interface in etomica.graph.engine
-
- parser - Variable in class etomica.modules.render.RenderMD
-
- Parser - Class in org.jmol.util
-
- Parser() - Constructor for class org.jmol.util.Parser
-
- Parser.Assignment - Interface in etomica.graph.engine
-
- Parser.BinaryOp - Interface in etomica.graph.engine
-
- Parser.BinaryOpByte - Interface in etomica.graph.engine
-
- Parser.Command - Interface in etomica.graph.engine
-
- Parser.CommandPropertyValue - Interface in etomica.graph.engine
-
- Parser.CommandValue - Interface in etomica.graph.engine
-
- Parser.CommandVariable - Interface in etomica.graph.engine
-
- Parser.CommandVariableValue - Interface in etomica.graph.engine
-
- Parser.Constructor - Interface in etomica.graph.engine
-
- Parser.ConstructorColored - Interface in etomica.graph.engine
-
- Parser.ConstructorMono - Interface in etomica.graph.engine
-
- Parser.Expression - Interface in etomica.graph.engine
-
- Parser.ParserException - Exception in etomica.graph.engine
-
- Parser.Property - Interface in etomica.graph.engine
-
- Parser.Statement - Interface in etomica.graph.engine
-
- Parser.StrictExpression - Interface in etomica.graph.engine
-
- Parser.UnaryOp - Interface in etomica.graph.engine
-
- Parser.UnaryOpByte - Interface in etomica.graph.engine
-
- Parser.UnaryOpByteMap - Interface in etomica.graph.engine
-
- Parser.UnaryOpColor - Interface in etomica.graph.engine
-
- Parser.UnaryOpThreeColor - Interface in etomica.graph.engine
-
- Parser.UnaryOpTwoByte - Interface in etomica.graph.engine
-
- Parser.Value - Interface in etomica.graph.engine
-
- Parser.Variable - Interface in etomica.graph.engine
-
- parseRect(String) - Method in class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
-
- ParserException(String) - Constructor for exception etomica.graph.engine.Parser.ParserException
-
- ParserException(String, Throwable) - Constructor for exception etomica.graph.engine.Parser.ParserException
-
- ParserImpl - Class in etomica.graph.engine.impl
-
- ParserImpl() - Constructor for class etomica.graph.engine.impl.ParserImpl
-
- ParserLAMMPS - Class in etomica.parser
-
- ParserLAMMPS() - Constructor for class etomica.parser.ParserLAMMPS
-
- ParserLAMMPS.Options - Class in etomica.parser
-
- ParserLAMMPS.Stuff - Class in etomica.parser
-
- ParserLAMMPS.Truncation - Enum in etomica.parser
-
- parsers - Variable in class etomica.util.ParameterBase
-
- parseStringInfestedFloatArray(String, BitSet, float[]) - Static method in class org.jmol.util.Parser
-
parses a "dirty" string for floats.
- parseToken(String) - Static method in class org.jmol.util.Parser
-
- parseTokenNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseTokenRange(String, int, int[]) - Static method in class org.jmol.util.Parser
-
- parseTrimmed(String) - Static method in class org.jmol.util.Parser
-
- parseTrimmedAt(String, int) - Static method in class org.jmol.util.Parser
-
- parseTrimmedRange(String, int, int) - Static method in class org.jmol.util.Parser
-
- PARTIAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
-
- PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
-
- PARTIAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
-
- PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
-
- partialcharge - Static variable in class org.jmol.script.Token
-
- partialdots - Static variable in class org.jmol.script.Token
-
- particleCounters - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- particles - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- PartitionedIterator - Class in etomica.graph.iterators
-
- PartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) - Constructor for class etomica.graph.iterators.PartitionedIterator
-
- partitions - Variable in class etomica.virial.ClusterSinglyConnected
-
- partitionsA - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- partitionsC - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- PartitionsP - Class in etomica.veos.bigdecimal
-
Number of partitions.
- PartitionsP() - Constructor for class etomica.veos.bigdecimal.PartitionsP
-
Default constructor initializing a list of partitions up to 7.
- partnerColor - Variable in class etomica.graphics.ColorSchemeColliders
-
Color applied to the upList atom of the colliding pair
- partners - Variable in class etomica.atom.iterator.ApiIndexList
-
- pascal() - Static method in class etomica.math.SpecialFunctions
-
- pascal() - Static method in class etomica.potential.P2O2Bartolomei
-
- Pascal - Class in etomica.units
-
The Pascal unit of pressure, equal to 1 N/m^2.
- path - Static variable in class org.jmol.script.Token
-
- pathforallfiles - Static variable in class org.jmol.script.Token
-
- pause() - Method in class etomica.action.activity.ActivityGroupParallel
-
- pause() - Method in class etomica.action.activity.ActivityGroupSeries
-
Requests a pause in the performance of the actions.
- pause() - Method in class etomica.action.Activity
-
Requests that the Activity pause its execution.
- pause - Static variable in class org.jmol.script.Token
-
- pauseAfterEachAction - Variable in class etomica.action.activity.ActivityGroupSeries
-
- pauseRequested - Variable in class etomica.action.Activity
-
- pbuf - Variable in class org.jmol.g3d.Graphics3D
-
- pbufT - Variable in class org.jmol.g3d.Graphics3D
-
- pBW - Variable in class etomica.interfacial.LJMC
-
- pBW - Variable in class etomica.interfacial.LJMD
-
- pc - Variable in class etomica.data.meter.MeterPressureTensor
-
- pc - Variable in class etomica.data.meter.MeterRDFPC
-
- pc - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- pc - Variable in class etomica.interfacial.MeterWallForce
-
- pc - Variable in class etomica.liquidLJ.MeterPUCut
-
- pc - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- pc - Variable in class etomica.mappedvirial.MeterMappedU
-
- pc - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- pc - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- pc - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- pc - Variable in class etomica.modules.materialfracture.MeterLoad
-
- pc - Variable in class etomica.modules.materialfracture.MeterStress
-
- pc - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pc - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- pc - Variable in class etomica.modules.sam.MeterWallPressure
-
- pc - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- pc - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- pc - Variable in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- pCalc(int, double[], double) - Method in class etomica.veos.QSeries
-
Computes the pressure via dlnQ/dV based on the volume series for Q given by coeffQ.
- pCalc(double, double) - Method in class etomica.veos.Ushcats
-
- pcDADv2 - Variable in class etomica.liquidLJ.MeterPUCut
-
- pcDADv2 - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- pCenter - Variable in class etomica.normalmode.MeterDDP
-
- pCenter - Variable in class etomica.normalmode.MeterDP
-
- pcForce - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- pcForce - Variable in class etomica.mappedvirial.MeterMappedU
-
- pcForce - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- pcForce - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- pcForce - Variable in class etomica.mappedvirial.MeterMeanForce
-
- pcForce - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- pcForceSum - Variable in class etomica.normalmode.MeterDADB
-
- pcForceSum - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- pcGB - Variable in class etomica.dimer.SimDimerMEAMGB
-
- pcom - Variable in class etomica.util.numerical.Function1d
-
- PCopy - Class in etomica.graph.operations
-
- PCopy() - Constructor for class etomica.graph.operations.PCopy
-
- pCross - Variable in class etomica.normalmode.HSNPT
-
- pdbaddhydrogens - Static variable in class org.jmol.script.Token
-
- pdbgetheader - Static variable in class org.jmol.script.Token
-
- pdbsequential - Static variable in class org.jmol.script.Token
-
- PDBWriter - Class in etomica.action
-
Action that dumps a box's configuration to an PDB file.
- PDBWriter() - Constructor for class etomica.action.PDBWriter
-
- PDBWriter(IBox) - Constructor for class etomica.action.PDBWriter
-
- PDF - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PDF_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PDF_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PDF_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PE(IVector) - Method in interface etomica.api.IVectorMutable
-
Plus-equals (+=) operation.
- PE(double) - Method in interface etomica.api.IVectorMutable
-
Plus-equals (+=) operation, causing a constant value to be added to all
components of this vector.
- PE(IData) - Method in interface etomica.data.IData
-
Plus-equals (+=) operation.
- PE(double) - Method in interface etomica.data.IData
-
Plus-equals (+=) operation, adding given value to all values in data.
- PE(IData) - Method in class etomica.data.types.DataDouble
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataDouble
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataDoubleArray
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataDoubleArray
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataDoubleBDArray
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataDoubleBDArray
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataGroup
-
- PE(double) - Method in class etomica.data.types.DataGroup
-
- PE(IData) - Method in class etomica.data.types.DataTensor
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataTensor
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataVector
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataVector
-
Plus-equals (+=) operation.
- PE(Quaternion) - Method in class etomica.math.Quaternion
-
Adds the input Quaternion components to its components.
- PE(double) - Method in interface etomica.space.Tensor
-
- PE(Tensor) - Method in interface etomica.space.Tensor
-
- PE(int, int, double) - Method in interface etomica.space.Tensor
-
- PE(double) - Method in class etomica.space1d.Tensor1D
-
- PE(int, int, double) - Method in class etomica.space1d.Tensor1D
-
- PE(Tensor) - Method in class etomica.space1d.Tensor1D
-
- PE(double) - Method in class etomica.space1d.Vector1D
-
- PE(IVector) - Method in class etomica.space1d.Vector1D
-
- PE(double) - Method in class etomica.space2d.Tensor2D
-
- PE(Tensor) - Method in class etomica.space2d.Tensor2D
-
- PE(int, int, double) - Method in class etomica.space2d.Tensor2D
-
- PE(IVector) - Method in class etomica.space2d.Vector2D
-
- PE(double) - Method in class etomica.space2d.Vector2D
-
- PE(double) - Method in class etomica.space3d.Tensor3D
-
- PE(Tensor) - Method in class etomica.space3d.Tensor3D
-
- PE(int, int, double) - Method in class etomica.space3d.Tensor3D
-
- PE(IVector) - Method in class etomica.space3d.Vector3D
-
- PE(double) - Method in class etomica.space3d.Vector3D
-
- PE(double) - Method in class etomica.spaceNd.TensorND
-
- PE(Tensor) - Method in class etomica.spaceNd.TensorND
-
- PE(int, int, double) - Method in class etomica.spaceNd.TensorND
-
- PE(IVector) - Method in class etomica.spaceNd.VectorND
-
- PE(double) - Method in class etomica.spaceNd.VectorND
-
- PE(IBigValue) - Method in class etomica.veos.BigValue
-
Plus-equals (+=) operation.
- PE(IBigValue) - Method in interface etomica.veos.IBigValue
-
Plus-equals (+=) operation.
- PE(IBigValue) - Method in class etomica.veos.MyBigDecimal
-
Plus-equals (+=) operation.
- PEa1Tt1(double, Tensor) - Method in interface etomica.space.Tensor
-
- PEa1Tt1(double, Tensor) - Method in class etomica.space1d.Tensor1D
-
- PEa1Tt1(double, Tensor) - Method in class etomica.space2d.Tensor2D
-
- PEa1Tt1(double, Tensor) - Method in class etomica.space3d.Tensor3D
-
- PEa1Tt1(double, Tensor) - Method in class etomica.spaceNd.TensorND
-
- PEa1Tv1(double, IVector) - Method in interface etomica.api.IVectorMutable
-
Increments (+=) components by (a1 * v1)
- PEa1Tv1(double, IVector) - Method in class etomica.space1d.Vector1D
-
- PEa1Tv1(double, IVector) - Method in class etomica.space2d.Vector2D
-
- PEa1Tv1(double, IVector) - Method in class etomica.space3d.Vector3D
-
- PEa1Tv1(double, IVector) - Method in class etomica.spaceNd.VectorND
-
- PEa1Tv1(double, IBigValue) - Method in class etomica.veos.BigValue
-
Plus-equals (+=) a1 times v1.
- PEa1Tv1(double, IBigValue) - Method in interface etomica.veos.IBigValue
-
Plus-equals (+=) a1 times v1.
- PEa1Tv1(double, IBigValue) - Method in class etomica.veos.MyBigDecimal
-
Plus-equals (+=) a1 times v1.
- peek() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- peek() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Returns the next iterate without advancing the iterator.
- peek() - Method in interface etomica.lattice.SiteIterator
-
Returns the next iterate without advancing the iterator.
- PENDING - Static variable in class etomica.action.activity.Controller.ActionStatus
-
- pendingActions - Variable in class etomica.action.activity.ActivityGroupSeries
-
- Percent - Class in etomica.units
-
Decimal representation of something that represents the fractional
amount of a whole (e.g., mole fraction) as a percentage value typically
between 0 and 100.
- percent - Static variable in class org.jmol.script.Token
-
- percentvdwatom - Static variable in class org.jmol.script.Token
-
- PercusYevick - Class in etomica.virial
-
Calculates the Percus-Yevick (PY) virial coefficients of second to Mth order for any spherically-symmetric Mayer function, fr.
- PercusYevick() - Constructor for class etomica.virial.PercusYevick
-
- PercusYevick1QC - Class in etomica.virial
-
Computes the Percus-Yevick compressibility-route approximation to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).
- PercusYevick1QC() - Constructor for class etomica.virial.PercusYevick1QC
-
- periodicity - Variable in class etomica.nbr.cell.Api1ACell
-
- periodicity - Variable in class etomica.nbr.cell.ApiAACell
-
- periodicity - Variable in class etomica.nbr.cell.molecule.Mpi1ACell
-
- periodicity - Variable in class etomica.nbr.cell.molecule.MpiAACell
-
- periodicity - Variable in class etomica.nbr.site.Api1ASite
-
- PermutationDegenerateIterator - Class in etomica.math.discrete
-
Iterator that returns unique permutations of an array of integers, with
degeneracy such that some of the integers may appear more than once in the array.
- PermutationDegenerateIterator(int) - Constructor for class etomica.math.discrete.PermutationDegenerateIterator
-
Constructs instance whose iterates are int[] of length n.
- PermutationIterator - Class in etomica.math.discrete
-
Iterator that returns different permutations of a sequence of integers when
called in successive iterations.
- PermutationIterator(int) - Constructor for class etomica.math.discrete.PermutationIterator
-
- PermutationIterator - Class in etomica.virial.cluster
-
- PermutationIterator(int[]) - Constructor for class etomica.virial.cluster.PermutationIterator
-
- permutations - Variable in class etomica.virial.ClusterBonds
-
- Permutator - Interface in etomica.graph.model
-
- perParticleFrequency - Variable in class etomica.integrator.mcmove.MCMoveBox
-
Flag indicating whether nominal frequency is interpreted as a
perParticleFrequency, or as a full frequency.
- perspective(int, float) - Method in class g3dsys.control.G3DSys
-
Handles perspective based on depth and diameter.
- perspectivedepth - Static variable in class org.jmol.script.Token
-
- perspectivemodel - Static variable in class org.jmol.script.Token
-
- pEst - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- PETA - Static variable in class etomica.units.Prefix
-
Prefix indicating 10+15.
- PEv1v2(IVector, IVector) - Method in interface etomica.space.Tensor
-
Increments this by the dyadic or outer product of the given vectors.
- PEv1v2(IVector, IVector) - Method in class etomica.space1d.Tensor1D
-
- PEv1v2(IVector, IVector) - Method in class etomica.space2d.Tensor2D
-
- PEv1v2(IVector, IVector) - Method in class etomica.space3d.Tensor3D
-
- PEv1v2(IVector, IVector) - Method in class etomica.spaceNd.TensorND
-
- pFast - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- pFF - Variable in class etomica.interfacial.LJMC
-
- pFF - Variable in class etomica.interfacial.LJMD
-
- pFull - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- pHarmonic - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pHarmonic - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- phaseAngles - Variable in class etomica.normalmode.NormalModesVariable
-
- phi(int, double) - Static method in class etomica.densityofstate.CopyOfOrthogonalPolynomial
-
- phi(int, double, double) - Static method in class etomica.densityofstate.OrthogonalPolynomial
-
- PHI - Static variable in class etomica.meam.PotentialMEAM
-
- phi - Static variable in class org.jmol.script.Token
-
- phi2Sum - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- phiData - Variable in class etomica.data.meter.MeterDihedralAngle
-
- phiEq - Variable in class etomica.potential.P4TorsionDreiding
-
- phiSlider - Variable in class etomica.modules.sam.SamGraphic
-
- phiSum - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- phongexponent - Static variable in class org.jmol.script.Token
-
- phongExponent - Static variable in class org.jmol.util.Shader
-
- pi - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- pi(MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Euler's constant.
- pi(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
return the count of primes <= n
- picking - Static variable in class org.jmol.script.Token
-
- pickingspinrate - Static variable in class org.jmol.script.Token
-
- pickingstyle - Static variable in class org.jmol.script.Token
-
- picklabel - Static variable in class org.jmol.script.Token
-
- PICO - Static variable in class etomica.units.Prefix
-
Prefix indicating 10-12.
- Picosecond - Class in etomica.units
-
Simulation unit of time.
- pidOf(Object) - Static method in enum org.jmol.constant.EnumPalette
-
- PINK - Static variable in class org.jmol.util.Colix
-
- PistonCylinder - Class in etomica.modules.pistoncylinder
-
Simple hard-sphere MD in piston-cylinder apparatus
- PistonCylinder(int) - Constructor for class etomica.modules.pistoncylinder.PistonCylinder
-
- PistonCylinderGraphic - Class in etomica.modules.pistoncylinder
-
- PistonCylinderGraphic(PistonCylinder, ISpace) - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Creates a PistonCylinder graphic instance.
- PistonCylinderGraphic.Applet - Class in etomica.modules.pistoncylinder
-
- PistonCylinderGraphic.ModifierAtomDiameter - Class in etomica.modules.pistoncylinder
-
- PistonCylinderGraphic.ModifierPistonDensity - Class in etomica.modules.pistoncylinder
-
- PistonPlane - Class in etomica.modules.pistoncylinder
-
Wrap a P1HardMovingBoundary and make it look like a Plane.
- PistonPlane(ISpace, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.PistonPlane
-
- pistonPotential - Variable in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonPlane
-
- pistonUpdateRequested() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- pixel - Variable in class etomica.graphics.DisplayCanvas
-
- Pixel - Class in etomica.units
-
Unit converting between simulation unit of length and pixels rendered in an
image.
- Pixel() - Constructor for class etomica.units.Pixel
-
Constructs with default of 10 pixels per Angstrom.
- Pixel(double) - Constructor for class etomica.units.Pixel
-
Constructor for Pixel.
- pixelUnitToMillimeter - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Millimeters Per Pixel
- pixelX - Variable in class etomica.util.Grabber.CornerData
-
- pixelY - Variable in class etomica.util.Grabber.CornerData
-
- pj - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- pkl - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- pkl - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- pkl - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- PLANCK_H - Static variable in class etomica.util.Constants
-
Planck's constant, in simulation units.
- Plane - Class in etomica.math.geometry
-
Class describing a plane occupying a 3-dimensional space.
- Plane(ISpace) - Constructor for class etomica.math.geometry.Plane
-
Default constructor returns the y-z plane.
- Plane(Plane) - Constructor for class etomica.math.geometry.Plane
-
Constructs a new Plane as a copy of the given one.
- Plane(ISpace, double, double, double, double) - Constructor for class etomica.math.geometry.Plane
-
Constructs a Plane satisfying the equation a x + b y + c z + d = 0
- plane - Static variable in class org.jmol.script.Token
-
- PLat - Variable in class etomica.normalmode.MeterSolidProps
-
- PLat - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- Platform - Class in org.jmol.awt
-
- Platform() - Constructor for class org.jmol.awt.Platform
-
- play - Static variable in class org.jmol.script.Token
-
- playDumb - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- playrev - Static variable in class org.jmol.script.Token
-
- plgndr(int, int, double) - Static method in class etomica.util.AssociatedPolynomial
-
- plm(int, int, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- plmrb(double[][], double, int) - Method in class etomica.potential.P2HydrogenPatkowski
-
- plmrb(double[][], double, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- plot - Variable in class etomica.graphics.DisplayPlot
-
- plot - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- plot - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- plot - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- plot - Variable in class etomica.meam.MEAM_MC
-
- plot - Variable in class etomica.meam.MEAMMd3D
-
- Plot - Class in etomica.modules.clustergenerator
-
Used from comphys.graphic.plot
A class which makes plotting a little more convenient than using
Java's Graphics methods.
- Plot() - Constructor for class etomica.modules.clustergenerator.Plot
-
Constructor sets default size of the plot
- Plot(Color, int, int) - Constructor for class etomica.modules.clustergenerator.Plot
-
- plot - Variable in class etomica.simulation.prototypes.LjMd2D
-
- plot - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- plot - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- plot3d - Static variable in class org.jmol.script.Token
-
- plotAction - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- PlotAction(int) - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
-
- plotAction - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- PlotAction(int) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- plotBox(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotD - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotImage(int, int, int, Object, Graphics3D, short, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- plotImage(int, int, int, Image, Graphics3D, short, int, int) - Method in class org.jmol.util.GData
-
- plotImagePixel(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- plotLine(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotP - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotPanel - Variable in class etomica.graphics.SimulationPanel
-
- plotPixelClippedP3i(Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- plotRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plots - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- plotsPane - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotString(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotStringCenter(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotT - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotText(int, int, int, int, int, String, JmolFont, Graphics3D) - Method in class org.jmol.g3d.Graphics3D
-
- plotText(int, int, int, int, int, String, JmolFont, Graphics3D) - Method in class org.jmol.util.GData
-
- plus(Complex) - Method in class etomica.math.Complex
-
Addition of Complex numbers (doesn't change this Complex number).
- plus(Matrix) - Method in class etomica.math.linearalgebra.Matrix
-
- plus(Rational) - Method in class etomica.util.Rational
-
Returns a new Rational instance, which is the result of adding the given
Rational to this Rational.
- pmesh - Static variable in class org.jmol.script.Token
-
- pmlt - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- pmlt - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- pN2HellmannA - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- pNA - Variable in class etomica.virial.MayerFunctionNonAdditiveFull
-
- PNCO2GCPM - Class in etomica.models.co2
-
GCPM CO2 potential class (GCPCDO).
- PNCO2GCPM(ISpace) - Constructor for class etomica.models.co2.PNCO2GCPM
-
- PNCO2GCPM(ISpace, int) - Constructor for class etomica.models.co2.PNCO2GCPM
-
- PNCO2GCPM.Component - Enum in etomica.models.co2
-
- PNCO2GCPM.P3GCPMAxilrodTeller - Class in etomica.models.co2
-
- PNG - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNG_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNG_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNGCPM - Class in etomica.models.co2
-
Generic GCPM potential class, capable of handling both CO2 and water.
- PNGCPM(ISpace, AtomTypeAgentManager, int) - Constructor for class etomica.models.co2.PNGCPM
-
- PNGCPM(ISpace, AtomTypeAgentManager, int, int) - Constructor for class etomica.models.co2.PNGCPM
-
- PNGCPM.Component - Enum in etomica.models.co2
-
- PNGCPM.GCPMAgent - Class in etomica.models.co2
-
- PNGCPM.P3GCPMAxilrodTeller - Class in etomica.models.co2
-
- PNGCPM.PNGCPMCached - Class in etomica.models.co2
-
- PNGCPMCached() - Constructor for class etomica.models.co2.PNGCPM.PNGCPMCached
-
- PNGCPMX - Class in etomica.models.co2
-
GCPM potential that allows combining parameters to be adjusted.
- PNGCPMX(ISpace, AtomTypeAgentManager, int, double, double, double) - Constructor for class etomica.models.co2.PNGCPMX
-
- PNGCPMX(ISpace, AtomTypeAgentManager, int, double, double, double, int) - Constructor for class etomica.models.co2.PNGCPMX
-
- PNWaterGCPM - Class in etomica.models.water
-
GCPM Water potential class.
- PNWaterGCPM(ISpace) - Constructor for class etomica.models.water.PNWaterGCPM
-
- PNWaterGCPMThreeSite - Class in etomica.models.water
-
GCPM Water potential with three association site for Wertheim approach.
- PNWaterGCPMThreeSite(ISpace, double, boolean, boolean) - Constructor for class etomica.models.water.PNWaterGCPMThreeSite
-
- PNWaterGCPMThreeSite(ISpace, double, boolean) - Constructor for class etomica.models.water.PNWaterGCPMThreeSite
-
- pochhammer(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Pochhammer's function.
- Pochhammer(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Compute Pochhammer's symbol (this)_n.
- Pochhammer(int) - Method in class etomica.veos.bigdecimal.Rational
-
Compute pochhammer's symbol (this)_n.
- Point - Class in etomica.math.geometry
-
A zero-dimensional polytope, a mathematical point in space.
- Point(ISpace) - Constructor for class etomica.math.geometry.Point
-
- Point(ISpace, IVectorMutable) - Constructor for class etomica.math.geometry.Point
-
- point - Static variable in class org.jmol.script.Token
-
- Point3f - Class in org.jmol.util
-
A 3 element point that is represented by single precision floating point
x,y,z coordinates.
- Point3f() - Constructor for class org.jmol.util.Point3f
-
- Point3fi - Class in org.jmol.util
-
the Point3fi class allows storage of critical information involving
an atom, picked bond, or measurement point, including:
xyz position
screen position
screen radius (-1 for a simple point)
index (for atoms or for an associated bond that has be picked)
associated modelIndex (for measurement points)
- Point3fi() - Constructor for class org.jmol.util.Point3fi
-
- Point3i - Class in org.jmol.util
-
A 3 element point that is represented by signed integer x,y,z coordinates.
- Point3i() - Constructor for class org.jmol.util.Point3i
-
- Point4f - Class in org.jmol.util
-
A 4 element point that is represented by single precision floating point
x,y,z,w coordinates.
- Point4f() - Constructor for class org.jmol.util.Point4f
-
Constructs and initializes a Point4f to (0,0,0,0).
- pointCharges - Variable in class etomica.models.rowley.ConformationEthanol
-
- pointCharges - Variable in class etomica.models.rowley.ConformationMethanol
-
- pointCharges - Static variable in class etomica.models.rowley.DimerApproach
-
- pointCharges - Variable in class etomica.models.rowley.SpeciesFactoryEthanol
-
- pointCharges - Variable in class etomica.models.rowley.SpeciesFactoryMethanol
-
- pointCharges - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- pointCount() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- pointCount() - Method in interface etomica.virial.ClusterAbstract
-
Number of points in the cluster.
- pointCount() - Method in class etomica.virial.ClusterBonds
-
- pointCount() - Method in class etomica.virial.ClusterChainHS
-
- pointCount() - Method in class etomica.virial.ClusterChainSoft
-
- pointCount() - Method in class etomica.virial.ClusterCoupledFlipped
-
- pointCount() - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- pointCount() - Method in class etomica.virial.ClusterDifference
-
- pointCount() - Method in class etomica.virial.ClusterExchange
-
- pointCount() - Method in class etomica.virial.ClusterSinglyConnected
-
- pointCount() - Method in class etomica.virial.ClusterSum
-
- pointCount() - Method in class etomica.virial.ClusterSumHS
-
- pointCount() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizable
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- pointCount() - Method in class etomica.virial.ClusterTree
-
- pointCount() - Method in class etomica.virial.ClusterWeightAbs
-
- pointCount() - Method in class etomica.virial.ClusterWeightSumWall
-
- pointCount() - Method in class etomica.virial.ClusterWeightUmbrella
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyHS
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoft
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoftBD
-
- pointgroupdistancetolerance - Static variable in class org.jmol.script.Token
-
- pointgrouplineartolerance - Static variable in class org.jmol.script.Token
-
- PointsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.PointsToggler
-
- Poise - Class in etomica.units
-
The Poise unit of viscosity, equal to 1 gram/(cm-sec).
- pol - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- polE1 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- polSite - Variable in class etomica.potential.P3Induction.MyAgent
-
- Polygon - Class in etomica.math.geometry
-
Representation of a mathematical polygon, a 2-dimensional polytope.
- Polygon(ISpace, int) - Constructor for class etomica.math.geometry.Polygon
-
Constructs a polygon with the given number of sides arranged in a closed loop.
- Polygon(LineSegment[]) - Constructor for class etomica.math.geometry.Polygon
-
Constructs a polygon using the given edges for its sides.
- polygonColixes - Variable in class org.jmol.util.MeshSurface
-
- polygonCount - Variable in class org.jmol.util.MeshSurface
-
- polygonCount0 - Variable in class org.jmol.util.MeshSurface
-
- PolygonGeneral - Class in etomica.math.geometry
-
TODO To change the template for this generated type comment go to Window -
Preferences - Java - Code Style - Code Templates
- PolygonGeneral(ISpace, int) - Constructor for class etomica.math.geometry.PolygonGeneral
-
- PolygonGeneral(LineSegment[]) - Constructor for class etomica.math.geometry.PolygonGeneral
-
- polygonIndexes - Variable in class org.jmol.util.MeshSurface
-
- polyhedra - Static variable in class org.jmol.script.Token
-
- Polyhedron - Class in etomica.math.geometry
-
Representation of a mathematical polyhedron, a 3-dimensional polytope.
- Polyhedron(Polygon[]) - Constructor for class etomica.math.geometry.Polyhedron
-
Constructs a polyhedron with the given faces for its sides.
- PolyhedronGeneral - Class in etomica.math.geometry
-
Representation of a mathematical polyhedron, a 3-dimensional polytope.
- PolyhedronGeneral(Polygon[]) - Constructor for class etomica.math.geometry.PolyhedronGeneral
-
- polymer - Static variable in class org.jmol.script.Token
-
- polymerlength - Static variable in class org.jmol.script.Token
-
- polymerList - Variable in class etomica.modules.sam.CriterionTether3
-
- polymerSpecies - Variable in class etomica.modules.sam.CriterionTether3
-
- PolynomialFit - Class in etomica.util.numerical
-
Class that performs a polynomial fit to x,y data, optionally taking weights
associated with each data point.
- PolynomialFit() - Constructor for class etomica.util.numerical.PolynomialFit
-
- polytope - Variable in class etomica.graphics.DisplayPolytope
-
- Polytope - Class in etomica.math.geometry
-
Representation of a mathematical polytope, which is a finite region of space
enclosed by a finite number of hyperplanes.
- Polytope(Polytope[]) - Constructor for class etomica.math.geometry.Polytope
-
Constructs a polytope of dimension D from the D-1 finite "planes" that
constitute it.
- populate(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperBranched
-
- populate(AtomArrayList, IAtom, IAtom, boolean) - Method in class etomica.association.AssociationHelperDouble
-
- populate(MoleculeArrayList, IMolecule, boolean) - Method in class etomica.association.AssociationHelperMolecule
-
- populateArrays(int, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- populateArrays(int, boolean) - Method in class etomica.overlap.DataOverlap
-
- populateBonds(Graph, List<ClusterBonds>, List<Double>, boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- populateEFBonds(Graph, List<ClusterBonds>, List<Double>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- populateEFBonds(Graph, List<ClusterBonds>, List<Double>, int, int, boolean, boolean, int) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- populateEFdfdTBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- populateEFdfdTdf2dT2Bonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperBranched
-
- populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperDouble
-
- populateList(MoleculeArrayList, IMolecule, boolean) - Method in class etomica.association.AssociationHelperMolecule
-
- populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperSingle
-
- populateList(AtomArrayList, IAtom, boolean) - Method in interface etomica.association.IAssociationHelper
-
Populates smerList with all atoms in the smer that contains atom.
- populateList(MoleculeArrayList, IMolecule, boolean) - Method in interface etomica.association.IAssociationHelperMolecule
-
Populates smerList with all molecules in the smer that contains molecule.
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveAtomMonomer
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveAtomSmer
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveBiasUB
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveRotateAssociated
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveSmer
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveSmerRotate
-
- populateList(AtomArrayList, IAtom) - Method in class etomica.association.MCMoveVolumeAssociated
-
- populateVDWDiameters(DiameterHashByElement) - Static method in class etomica.atom.DiameterHashByElement
-
Populates the given instance with diameters based on atomic radii
(taken from various sources).
- PopupListener(JPopupMenu) - Constructor for class etomica.graphics.DisplayPlot.PopupListener
-
- popupMenu - Variable in class etomica.graphics.DisplayPlot.PopupListener
-
- poreCenter - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- pos - Variable in class etomica.models.co2.P2CO2Hellmann
-
- pos - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- pos - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- pos - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- pos - Variable in class etomica.normalmode.MeterPlaneSlip
-
- pos - Variable in class etomica.potential.P2NitrogenHellmann
-
- pos - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
-
- pos - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- posA - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- posB - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- position - Variable in class etomica.atom.Atom
-
- position(IMolecule) - Method in class etomica.atom.AtomPositionCOM
-
- position(IMolecule) - Method in class etomica.atom.AtomPositionFirstAtom
-
- position(IMolecule) - Method in class etomica.atom.AtomPositionGeometricCenter
-
- position(IMolecule) - Method in class etomica.atom.AtomPositionGeometricCenterAlkaneEH
-
- position(IMolecule) - Method in class etomica.atom.AtomPositionGeometricCenterPBC
-
- position(IMolecule) - Method in interface etomica.atom.IAtomPositionDefinition
-
Returns the defined position for the given atom, which
may be an atom group.
- position - Variable in class etomica.atom.MoleculeOriented
-
- position - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- position - Variable in class etomica.data.meter.MeterProfileByVolume
-
- position - Variable in class etomica.math.geometry.Polytope
-
- position - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- position - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
-
- positionDefinition(IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- positionDefinition - Variable in class etomica.config.ConfigurationLattice
-
- positionDefinition - Variable in class etomica.data.meter.MeterProfileByVolume
-
- positionDefinition - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- positionDefinition - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- positionDefinition - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- positionDefinition - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- positionDefinition - Variable in class etomica.models.water.P2Water4P
-
- positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- positionDefinition - Variable in class etomica.modules.rosmosis.MeterFlux
-
- positionDefinition - Variable in class etomica.modules.sam.Sam
-
- positionDefinition - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- positionDefinition - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- positionDefinition - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- positionDefinition - Variable in class etomica.nbr.cell.NeighborCellManager
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- positionDefinition - Variable in class etomica.potential.P2MoleculeTruncated
-
- positionDefinition - Variable in class etomica.potential.P2ReactionFieldDipole
-
- positionDefinition - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- positionDefinition - Variable in class etomica.potential.PotentialGroupSoft
-
- positionDefinition - Variable in class etomica.virial.ClusterCoupledFlipped
-
- positionDefinition - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- positionDefinition - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- positionDefinition - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- positionDefinition - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- positionOld - Variable in class etomica.models.hexane.MCMoveCBMC
-
- positions - Variable in class etomica.dimer.SimDimerLJadatom
-
- positions - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- positions - Variable in class etomica.dimer.SimDimerMEAMGB
-
- positions - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- positions - Variable in class etomica.virial.CoordinatePairLeafSet
-
- positionSelectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- positionSource - Variable in class etomica.data.meter.MeterProfile
-
- positionSource - Variable in class etomica.data.meter.MeterWidomInsertion
-
- positionSource - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- positionSource - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- positionSource - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- positionSource - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- positionSource - Variable in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- positionVector - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- positionVector - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- posVec - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- posVecToAtoms(IVectorMutable[], IVectorMutable[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- pot - Variable in class etomica.virial.PotentialCommonAtomic
-
- poten() - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- potential - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- potential - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- potential - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- potential - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- potential - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- potential - Variable in class etomica.data.meter.MeterEnergy
-
- potential - Variable in class etomica.data.meter.MeterPotentialEnergy
-
- potential - Variable in class etomica.densityofstate.DensityOfState
-
- potential - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- potential - Variable in class etomica.dimer.EnergyMap
-
- potential - Variable in class etomica.dimer.SimDimerLJgb
-
- potential - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potential - Variable in class etomica.dimer.SimDimerMEAMGB
-
- potential - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- potential - Variable in class etomica.freeenergy.npath.SimLJ
-
- potential - Variable in class etomica.integrator.mcmove.MCMove
-
- potential - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- potential - Variable in class etomica.liquidLJ.LjMC3D
-
- potential - Variable in class etomica.liquidLJ.LjMd3D
-
- potential - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- potential - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- potential - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- potential - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- potential - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- potential - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- potential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- potential - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- potential - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- potential - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- potential - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- potential - Variable in class etomica.normalmode.LJVacancyMin
-
- potential - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- potential - Variable in class etomica.normalmode.MeterAPIPotentialEnergy
-
- potential - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- potential - Variable in class etomica.normalmode.SimHSMDVacancy
-
- potential - Variable in class etomica.normalmode.SimLJHTTISuper
-
- potential - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- potential - Variable in class etomica.normalmode.SimLJVacancy
-
- potential - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- potential - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- potential - Variable in class etomica.potential.P2MoleculeTruncated
-
- potential - Variable in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
-
- potential - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- potential - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- potential - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- Potential - Class in etomica.potential
-
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.
- Potential(int, ISpace) - Constructor for class etomica.potential.Potential
-
General constructor for a potential instance
- potential - Variable in class etomica.potential.PotentialGroup.PotentialLinker
-
- potential - Variable in class etomica.potential.PotentialMaster.PotentialLinker
-
- potential - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- potential - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- potential - Variable in class etomica.simulation.prototypes.HsMc2d
-
- potential - Variable in class etomica.simulation.prototypes.HSMD3D
-
The hard-sphere potential governing the interactions.
- potential - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- potential - Variable in class etomica.simulation.prototypes.LjMd2D
-
- potential - Variable in class etomica.simulation.prototypes.LjMd3D
-
- potential - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- potential - Variable in class etomica.simulation.prototypes.SwMd2D
-
- potential - Variable in class etomica.simulation.prototypes.SWMD3D
-
- potential - Variable in class etomica.spin.Heisenberg
-
- potential - Variable in class etomica.tests.TestLJMC3D
-
- potential - Variable in class etomica.thermointegration.LjMc3D
-
- potential - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- potential - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- potential - Variable in class etomica.threaded.PotentialThreaded
-
- potential - Variable in class etomica.virial.MayerGeneralAtomic
-
- potential - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- potential - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- potential - Variable in class etomica.yukawa.TestYukawaMC3D
-
- potential - Variable in class etomica.yukawa.TestYukawaMD3D
-
- Potential0 - Class in etomica.potential
-
Potential that does not depend on any atom positions.
- Potential0(ISpace) - Constructor for class etomica.potential.Potential0
-
- Potential0Lrc - Class in etomica.potential
-
Zero-body potential implementing the long-range correction
that compensates for truncation of the potential.
- Potential0Lrc(ISpace, IAtomType[], IPotentialAtomic) - Constructor for class etomica.potential.Potential0Lrc
-
- potential1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- Potential1 - Class in etomica.potential
-
Potential acting on a single atom or atom group.
- Potential1(ISpace) - Constructor for class etomica.potential.Potential1
-
- Potential1.Intramolecular - Interface in etomica.potential
-
Marker interface indicating that a one-body potential is an intramolecular
potential, and not, e.g., a potential of interaction with an external field.
- potential11 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potential11 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- potential12 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potential12 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- Potential2 - Class in etomica.potential
-
Potential acting on 2 atoms or molecules.
- Potential2(ISpace) - Constructor for class etomica.potential.Potential2
-
Constructs potential with given space.
- potential22 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potential22 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- Potential2HardSpherical - Class in etomica.potential
-
Methods for a hard (impulsive), spherically-symmetric pair potential.
- Potential2HardSpherical(ISpace) - Constructor for class etomica.potential.Potential2HardSpherical
-
- Potential2Soft - Interface in etomica.potential
-
Methods for properties obtained for a soft, differentiable pair potential.
- Potential2SoftSpherical - Class in etomica.potential
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSpherical(ISpace) - Constructor for class etomica.potential.Potential2SoftSpherical
-
- Potential2SoftSphericalLS - Class in etomica.potential
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLS(ISpace, double, double[], Potential2Soft) - Constructor for class etomica.potential.Potential2SoftSphericalLS
-
- Potential2SoftSphericalLSMulti - Class in etomica.liquidLJ
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLSMulti(ISpace, double[], Potential2Soft) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- Potential2SoftSphericalLSMultiLat - Class in etomica.liquidLJ
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLSMultiLat(ISpace, double[], Potential2Soft, CoordinateDefinition) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- Potential2SoftSphericalLSMultiLat.ReturnValue - Class in etomica.liquidLJ
-
- Potential2SoftSphericalLSMultiLatSlanty - Class in etomica.liquidLJ
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLSMultiLatSlanty(ISpace, double[], Potential2Soft, CoordinateDefinition, int[]) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- Potential2Spherical - Interface in etomica.potential
-
interface for spherical 2-body potentials
- potentialA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- potentialA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- potentialAA - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- potentialAA - Variable in class etomica.modules.mu.Mu
-
- potentialAA - Variable in class etomica.modules.osmosis.OsmosisSim
-
- potentialAB - Variable in class etomica.modules.mu.Mu
-
- potentialAB - Variable in class etomica.modules.osmosis.OsmosisSim
-
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in interface etomica.api.IPotentialMaster
-
Notifies the PotentialMaster that the sub-potential has been added to
the given PotentialGroup, which is associated (but not necessarily held
by) this PotentialMaster.
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.nbr.PotentialMasterHybrid
-
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.nbr.PotentialMasterNbr
-
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.potential.PotentialMaster
-
- potentialAgentManager - Variable in class etomica.potential.PotentialMasterMonatomic
-
- PotentialAndIterator(IPotentialAtomic, AtomsetIteratorBasisDependent) - Constructor for class etomica.chem.models.Model.PotentialAndIterator
-
- PotentialArray - Class in etomica.potential
-
Instances of this class are created by AtomType classes to
store the list of potentials and criteria that apply to
the atoms of that type.
- PotentialArray() - Constructor for class etomica.potential.PotentialArray
-
- PotentialArrayByType - Class in etomica.potential
-
This class stores an array of Potentials and remembers the "other" IAtomType
that the IPotential applies to.
- PotentialArrayByType() - Constructor for class etomica.potential.PotentialArrayByType
-
- PotentialArrayMolecular - Class in etomica.potential
-
Instances of this class are created by MoleculeType classes to
store the list of potentials and criteria that apply to
the molecules of that type.
- PotentialArrayMolecular() - Constructor for class etomica.potential.PotentialArrayMolecular
-
- potentialAtomic - Variable in class etomica.potential.PotentialMolecularMonatomic
-
- PotentialAtomicSum - Class in etomica.potential
-
Atomic potential class that simply sums up contributions from multiple
(atomic) potentials.
- PotentialAtomicSum(IPotentialAtomic[]) - Constructor for class etomica.potential.PotentialAtomicSum
-
- potentialAtt - Variable in class etomica.virial.MayerPTAtt
-
- potentialAtt - Variable in class etomica.virial.MayerSphericalPTAtt
-
- potentialB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- potentialB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- potentialBB - Variable in class etomica.modules.mu.Mu
-
- potentialBB - Variable in class etomica.modules.osmosis.OsmosisSim
-
- potentialBonded - Variable in class etomica.modules.render.RenderMD
-
- PotentialCalculation - Interface in etomica.potential
-
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.
- PotentialCalculationEFSSP - Class in etomica.normalmode
-
- PotentialCalculationEFSSP(ISpace, IBox, CoordinateDefinition, double, double, boolean) - Constructor for class etomica.normalmode.PotentialCalculationEFSSP
-
- PotentialCalculationEnergies() - Constructor for class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- PotentialCalculationEnergySum - Class in etomica.potential
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationEnergySum() - Constructor for class etomica.potential.PotentialCalculationEnergySum
-
- PotentialCalculationEnergySumBigDecimal - Class in etomica.potential
-
Mimics original PotentialEnergySum calculation, but uses a BigDecimal
representation for the sum.
- PotentialCalculationEnergySumBigDecimal(int) - Constructor for class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- PotentialCalculationEnergySumCutoff - Class in etomica.liquidLJ
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationEnergySumCutoff(ISpace, double[]) - Constructor for class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- PotentialCalculationForcePressureSum - Class in etomica.potential
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationForcePressureSum(ISpace) - Constructor for class etomica.potential.PotentialCalculationForcePressureSum
-
- PotentialCalculationForcePressureSumGB - Class in etomica.dimer
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationForcePressureSumGB(ISpace, IBox) - Constructor for class etomica.dimer.PotentialCalculationForcePressureSumGB
-
- PotentialCalculationForceStress - Class in etomica.modules.materialfracture
-
- PotentialCalculationForceStress(ISpace) - Constructor for class etomica.modules.materialfracture.PotentialCalculationForceStress
-
- PotentialCalculationForceSum - Class in etomica.potential
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationForceSum() - Constructor for class etomica.potential.PotentialCalculationForceSum
-
- PotentialCalculationForceSumThreaded - Class in etomica.threaded
-
- PotentialCalculationForceSumThreaded(PotentialCalculationForceSum[], ISpace) - Constructor for class etomica.threaded.PotentialCalculationForceSumThreaded
-
- PotentialCalculationForceSumWall - Class in etomica.modules.sam
-
- PotentialCalculationForceSumWall(P1WCAWall) - Constructor for class etomica.modules.sam.PotentialCalculationForceSumWall
-
- PotentialCalculationForceSumWallForce - Class in etomica.modules.rosmosis
-
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
- PotentialCalculationForceSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
- PotentialCalculationHyperVirialSum - Class in etomica.potential
-
Evaluates the hypervirial summed over all iterated atoms.
- PotentialCalculationHyperVirialSum() - Constructor for class etomica.potential.PotentialCalculationHyperVirialSum
-
- PotentialCalculationLJSP - Class in etomica.normalmode
-
- PotentialCalculationLJSP(ISpace, IBox, CoordinateDefinition, double, double, double, double, double) - Constructor for class etomica.normalmode.PotentialCalculationLJSP
-
- PotentialCalculationMappedVirial - Class in etomica.mappedvirial
-
PotentialCalculation that implements mapped-averaged virial (to get the
pressure).
- PotentialCalculationMappedVirial(ISpace, IBox, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- PotentialCalculationMappedVirialV - Class in etomica.mappedvirial
-
PotentialCalculation that implements mapped-averaged virial (to get the
pressure).
- PotentialCalculationMappedVirialV(ISpace, IBox, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- PotentialCalculationMappedVirialV.UShift - Class in etomica.mappedvirial
-
- PotentialCalculationMappedVirialV.USine - Class in etomica.mappedvirial
-
- PotentialCalculationMappedVirialV.VFunc - Interface in etomica.mappedvirial
-
- PotentialCalculationMolecular - Interface in etomica.potential
-
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.
- PotentialCalculationMolecularVirialSum - Class in etomica.potential
-
Evaluates the virial summed over all iterated molecules.
- PotentialCalculationMolecularVirialSum() - Constructor for class etomica.potential.PotentialCalculationMolecularVirialSum
-
- PotentialCalculationPhiSum - Class in etomica.potential
-
- PotentialCalculationPhiSum(ISpace) - Constructor for class etomica.potential.PotentialCalculationPhiSum
-
- PotentialCalculationPressureTensor - Class in etomica.potential
-
Calculates the pressure tensor by calculating the force on each atom, along
with including the kinetic portion (from the velocities or an Integrator).
- PotentialCalculationPressureTensor(ISpace) - Constructor for class etomica.potential.PotentialCalculationPressureTensor
-
- PotentialCalculationRDF - Class in etomica.data.meter
-
PotentialCalculation that simply does the work of collecting an RDF.
- PotentialCalculationRDF(ISpace, IBox) - Constructor for class etomica.data.meter.PotentialCalculationRDF
-
- PotentialCalculationSolidSuper - Class in etomica.normalmode
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationSolidSuper(ISpace, CoordinateDefinition) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuper
-
- PotentialCalculationSolidSuperCut - Class in etomica.normalmode
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationSolidSuperCut(ISpace, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- PotentialCalculationSolidSuperCutLS - Class in etomica.normalmode
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationSolidSuperCutLS(ISpace, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuperCutLS
-
- PotentialCalculationSumCutoff - Class in etomica.liquidLJ
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationSumCutoff(ISpace, double[]) - Constructor for class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- PotentialCalculationSumCutoffLS - Class in etomica.liquidLJ
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationSumCutoffLS() - Constructor for class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
- PotentialCalculationTorqueSum - Class in etomica.potential
-
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
- PotentialCalculationTorqueSum() - Constructor for class etomica.potential.PotentialCalculationTorqueSum
-
- PotentialCalculationTorqueSumWallForce - Class in etomica.modules.rosmosis
-
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
- PotentialCalculationTorqueSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- PotentialCalculationVirialSum - Class in etomica.potential
-
Evaluates the virial summed over all iterated atoms.
- PotentialCalculationVirialSum() - Constructor for class etomica.potential.PotentialCalculationVirialSum
-
- PotentialCalculationWallForce() - Constructor for class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- potentialCC - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialCC - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCC - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialChoice - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- potentialChooser - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialChooser - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialChooser - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialChooserListener - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialChooserListener - Variable in class etomica.modules.mu.MuGraphic
-
- potentialChooserListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialChooserListener - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialCHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialCHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialCN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialCO - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialCO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- PotentialCommonAtomic - Class in etomica.virial
-
- PotentialCommonAtomic(IPotentialAtomic) - Constructor for class etomica.virial.PotentialCommonAtomic
-
- PotentialCriterion() - Constructor for class etomica.atom.iterator.IteratorDirective.PotentialCriterion
-
- potentialCS - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialCS - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- PotentialCuLREP - Class in etomica.meam
-
- PotentialCuLREP(ISpace) - Constructor for class etomica.meam.PotentialCuLREP
-
- PotentialDLPOLY - Class in etomica.potential
-
- PotentialDLPOLY(ISpace) - Constructor for class etomica.potential.PotentialDLPOLY
-
- PotentialEFS - Class in etomica.meam
-
EFS (Extended Finnis-Sinclair) potential
- PotentialEFS(ISpace, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.meam.PotentialEFS
-
- PotentialEmul - Class in etomica.potential
-
PotentialEmul class invokes the emul external program to compute energies
between molecules.
- PotentialEmul(ISpace, String) - Constructor for class etomica.potential.PotentialEmul
-
- PotentialEmul(ISpace, String, double) - Constructor for class etomica.potential.PotentialEmul
-
- PotentialEmul(ISpace, String, int, double) - Constructor for class etomica.potential.PotentialEmul
-
- PotentialEmulCached - Class in etomica.virial
-
Potential class whose sole purpose is to remember previously calculated
energies and return them if no change has been made to the configuration.
- PotentialEmulCached(ISpace, String, int) - Constructor for class etomica.virial.PotentialEmulCached
-
- PotentialEmulCached(ISpace, String, double, int) - Constructor for class etomica.virial.PotentialEmulCached
-
- PotentialEmulCached(ISpace, String, int, double, int) - Constructor for class etomica.virial.PotentialEmulCached
-
- potentialES - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialES - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- PotentialFeEAM - Class in etomica.meam
-
EFS (Extended Finnis-Sinclair) potential
- PotentialFeEAM(ISpace, double, double, double, double, double, double) - Constructor for class etomica.meam.PotentialFeEAM
-
- PotentialFeEAM_LS - Class in etomica.meam
-
EFS (Extended Finnis-Sinclair) potential
- PotentialFeEAM_LS(CoordinateDefinition, ISpace, double, double, double, double, double, double, IVector[]) - Constructor for class etomica.meam.PotentialFeEAM_LS
-
- potentialGhost - Variable in class etomica.modules.insertion.Insertion
-
- PotentialGroup - Class in etomica.potential
-
Collection of potentials that act between the atoms contained in
one or more groups of atoms.
- PotentialGroup(int) - Constructor for class etomica.potential.PotentialGroup
-
Makes a potential group defined on the position of nBody atom or atom groups.
- PotentialGroup(int, ISpace) - Constructor for class etomica.potential.PotentialGroup
-
- PotentialGroup.PotentialLinker - Class in etomica.potential
-
- PotentialGroup3PI - Class in etomica.virial
-
PotentialGroup that calculates the energy between PI molecules triplets.
- PotentialGroup3PI(int) - Constructor for class etomica.virial.PotentialGroup3PI
-
- PotentialGroup3PI.PotentialGroup3PISkip - Class in etomica.virial
-
- PotentialGroup3PISkip(int) - Constructor for class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- PotentialGroupHybrid - Class in etomica.nbr
-
A PotentialGroup class to work with PotentialMasterHybrid.
- PotentialGroupHybrid(int) - Constructor for class etomica.nbr.PotentialGroupHybrid
-
- PotentialGroupNbr - Class in etomica.nbr
-
- PotentialGroupNbr(int) - Constructor for class etomica.nbr.PotentialGroupNbr
-
- PotentialGroupPI - Class in etomica.virial
-
PotentialGroup that calculates the energy between PI molecule pairs.
- PotentialGroupPI(int) - Constructor for class etomica.virial.PotentialGroupPI
-
- PotentialGroupPI.PotentialGroupPISkip - Class in etomica.virial
-
- PotentialGroupPISkip(int) - Constructor for class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- PotentialGroupSoft - Class in etomica.potential
-
include virial and gradient for a molecular potential
- PotentialGroupSoft(int, ISpace, double) - Constructor for class etomica.potential.PotentialGroupSoft
-
- PotentialHard - Interface in etomica.potential
-
Interface for hard potentials, having impulsive forces.
- potentialHpHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHpHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHpN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHpN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHS - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialHS - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialHS - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialHyHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHyHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHyN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHyO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialIdeal - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialIdeal - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialIterator - Variable in class etomica.potential.PotentialMasterMonatomic
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- PotentialLinker(IPotentialAtomic, AtomsetIteratorBasisDependent, IAtomType[], PotentialGroup.PotentialLinker) - Constructor for class etomica.potential.PotentialGroup.PotentialLinker
-
- PotentialLinker(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) - Constructor for class etomica.potential.PotentialMaster.PotentialLinker
-
- potentialList - Variable in class etomica.potential.PotentialMaster
-
- potentialLJ - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialLJClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJLS - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialLJLS - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- potentialLJNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialM1 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialM2 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialMaster - Variable in class etomica.AlkaneEH.CH4NVT
-
- potentialMaster - Variable in class etomica.AlkaneEH.DHS_NVT
-
- potentialMaster - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- potentialMaster - Variable in class etomica.association.MCMoveDimer
-
- potentialMaster - Variable in class etomica.association.MCMoveDimerRotate
-
- potentialMaster - Variable in class etomica.association.MCMoveSmer
-
- potentialMaster - Variable in class etomica.association.MCMoveSmerRotate
-
- potentialMaster - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- potentialMaster - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- potentialMaster - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- potentialMaster - Variable in class etomica.data.meter.MeterHyperVirial
-
- potentialMaster - Variable in class etomica.data.meter.MeterPressure
-
- potentialMaster - Variable in class etomica.data.meter.MeterPressureTensor
-
- potentialMaster - Variable in class etomica.data.meter.MeterRDFPC
-
- potentialMaster - Variable in class etomica.densityofstate.DensityOfState
-
- potentialMaster - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- potentialMaster - Variable in class etomica.dielectric.DHS_NVT
-
- potentialMaster - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- potentialMaster - Variable in class etomica.dielectric.TIP4P_NVT
-
- potentialMaster - Variable in class etomica.dimer.EnergyMap
-
- potentialMaster - Variable in class etomica.dimer.SimDimerLJadatom
-
- potentialMaster - Variable in class etomica.dimer.SimDimerLJgb
-
- potentialMaster - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potentialMaster - Variable in class etomica.dimer.SimDimerMEAMGB
-
- potentialMaster - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- potentialMaster - Variable in class etomica.integrator.IntegratorBox
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- potentialMaster - Variable in class etomica.interfacial.LJMD
-
- potentialMaster - Variable in class etomica.interfacial.MeterWallForce
-
- potentialMaster - Variable in class etomica.kmc.SimKMCLJadatom
-
- potentialMaster - Variable in class etomica.liquidLJ.MeterPU
-
- potentialMaster - Variable in class etomica.liquidLJ.MeterPUCut
-
- potentialMaster - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMappedU
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMeanForce
-
- potentialMaster - Variable in class etomica.meam.EFSTungsten
-
- potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- potentialMaster - Variable in class etomica.meam.MEAM_MC
-
- potentialMaster - Variable in class etomica.meam.MEAMMd3D
-
- potentialMaster - Variable in class etomica.metastable.LJmuVT
-
- potentialMaster - Variable in class etomica.metastable.LJNPT
-
- potentialMaster - Variable in class etomica.metastable.LJNVT
-
- potentialMaster - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialMaster - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- potentialMaster - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.rowley.DimerApproach
-
- potentialMaster - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- potentialMaster - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- potentialMaster - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- potentialMaster - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- potentialMaster - Variable in class etomica.modules.colloid.ColloidSim
-
- potentialMaster - Variable in class etomica.modules.droplet.DropletAtomic
-
- potentialMaster - Variable in class etomica.modules.mu.P1MagicWall
-
- potentialMaster - Variable in class etomica.modules.render.RenderMD
-
- potentialMaster - Variable in class etomica.modules.sam.ConfigurationSAM
-
- potentialMaster - Variable in class etomica.modules.sam.Sam
-
- potentialMaster - Variable in class etomica.modules.vle.MeterPressure2
-
- potentialMaster - Variable in class etomica.nbr.list.BoxAgentSourceCellManagerList
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.NeighborCellManagerList
-
- potentialMaster - Variable in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- potentialMaster - Variable in class etomica.nbr.list.NeighborListManager
-
- potentialMaster - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- potentialMaster - Variable in class etomica.normalmode.HessianDB
-
- potentialMaster - Variable in class etomica.normalmode.HSDimerNPT
-
- potentialMaster - Variable in class etomica.normalmode.HSNPT
-
- potentialMaster - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- potentialMaster - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- potentialMaster - Variable in class etomica.normalmode.LJVacancyMin
-
- potentialMaster - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- potentialMaster - Variable in class etomica.normalmode.MeterDADB
-
- potentialMaster - Variable in class etomica.normalmode.MeterDDP
-
- potentialMaster - Variable in class etomica.normalmode.MeterDP
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidDA
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidDACut
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidProps
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- potentialMaster - Variable in class etomica.normalmode.MeterTargetTP
-
- potentialMaster - Variable in class etomica.normalmode.MinimizeHCP
-
- potentialMaster - Variable in class etomica.normalmode.NormalModesMolecular
-
- potentialMaster - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSLJ
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep1
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep1HCP
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep2
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep2HCP
-
- potentialMaster - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- potentialMaster - Variable in class etomica.normalmode.SimLJHTTISuper
-
- potentialMaster - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- potentialMaster - Variable in class etomica.normalmode.SimLJVacancy
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- potentialMaster - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialMaster - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
- potentialMaster - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
- potentialMaster - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- potentialMaster - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- potentialMaster - Variable in class etomica.potential.P2SquareWellRobust
-
- potentialMaster - Variable in class etomica.potential.PotentialGroup
-
- PotentialMaster - Class in etomica.potential
-
Manager of all potentials in simulation.
- PotentialMaster() - Constructor for class etomica.potential.PotentialMaster
-
- PotentialMaster(IteratorFactory) - Constructor for class etomica.potential.PotentialMaster
-
- potentialMaster - Variable in class etomica.simulation.prototypes.HSMD3D
-
- potentialMaster - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- potentialMaster - Variable in class etomica.spin.Heisenberg
-
- potentialMaster - Variable in class etomica.surfacetension.LJMC
-
- potentialMaster - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- potentialMaster - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- potentialMaster - Variable in class etomica.util.numerical.CalcGradientDifferentiable
-
- PotentialMaster.AtomIterator0 - Class in etomica.potential
-
- PotentialMaster.MoleculeIterator0 - Class in etomica.potential
-
- PotentialMaster.PotentialLinker - Class in etomica.potential
-
- potentialMasterA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialMasterA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialMasterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialMasterB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialMasterB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialMasterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialMasterCell - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- potentialMasterCell - Variable in class etomica.freeenergy.npath.SimLJ
-
- potentialMasterCell - Variable in class etomica.interfacial.LJMC
-
- potentialMasterCell - Variable in class etomica.liquidLJ.LjMC3D
-
- PotentialMasterCell - Class in etomica.nbr.cell
-
A PotentialMaster for use with a Simulation where cell-listing of atoms and
their neighbors is appropriate.
- PotentialMasterCell(ISimulation, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
Creates PotentialMasterCell with default (1.0) range.
- PotentialMasterCell(ISimulation, double, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
Constructs with null AtomPositionDefinition, which indicates the position
definition given with each atom's AtomType should be used.
- PotentialMasterCell(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
- PotentialMasterCell(ISimulation, double, BoxAgentSourceCellManager, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
- PotentialMasterCell(ISimulation, double, BoxAgentSourceCellManager, BoxAgentManager<NeighborCellManager>, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
- potentialMasterCell - Variable in class etomica.nbr.PotentialGroupHybrid
-
- potentialMasterD - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potentialMasterD - Variable in class etomica.dimer.SimDimerMEAMGB
-
- potentialMasterD - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- potentialMasterDADv2 - Variable in class etomica.liquidLJ.MeterPUCut
-
- potentialMasterDADv2 - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- potentialMasterDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep1
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep1HCP
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep2
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep2HCP
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- PotentialMasterHybrid - Class in etomica.nbr
-
PotentialMaster that uses both neighbor-cell iteration and cell-list
iteration.
- PotentialMasterHybrid(ISimulation, double, ISpace) - Constructor for class etomica.nbr.PotentialMasterHybrid
-
Invokes superclass constructor, specifying IteratorFactoryCell
for generating molecule iterators.
- PotentialMasterHybrid(ISimulation, IAtomPositionDefinition, double, ISpace) - Constructor for class etomica.nbr.PotentialMasterHybrid
-
Constructs class using given position definition for all atom cell assignments.
- potentialMasterList - Variable in class etomica.liquidLJ.LjMd3D
-
- PotentialMasterList - Class in etomica.nbr.list
-
PotentialMaster used to implement neighbor listing.
- PotentialMasterList(ISimulation, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
-
Default constructor uses range of 1.0.
- PotentialMasterList(ISimulation, double, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
-
Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
- PotentialMasterList(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
-
Constructs class using given position definition for all atom cell
assignments.
- PotentialMasterList(ISimulation, double, BoxAgentSourceCellManagerList, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
-
- PotentialMasterList(ISimulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<? extends BoxCellManager>, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
-
- PotentialMasterList(ISimulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<? extends BoxCellManager>, PotentialMasterList.NeighborListAgentSource, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
-
- potentialMasterList - Variable in class etomica.nbr.PotentialGroupHybrid
-
- potentialMasterList - Variable in class etomica.normalmode.SimHSMDVacancy
-
- PotentialMasterList.NeighborListAgentSource - Class in etomica.nbr.list
-
- PotentialMasterListDimer - Class in etomica.dimer
-
- PotentialMasterListDimer(ISimulation, ISpace) - Constructor for class etomica.dimer.PotentialMasterListDimer
-
- PotentialMasterListMolecular - Class in etomica.nbr.list.molecule
-
PotentialMaster used to implement neighbor listing.
- PotentialMasterListMolecular(ISimulation, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Default constructor uses range of 1.0.
- PotentialMasterListMolecular(ISimulation, double, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
- PotentialMasterListMolecular(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Constructs class using given position definition for all atom cell
assignments.
- PotentialMasterListMolecular(ISimulation, double, BoxAgentSourceCellManagerListMolecular, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- PotentialMasterListMolecular(ISimulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- PotentialMasterListMolecular(ISimulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, PotentialMasterListMolecular.NeighborListAgentSourceMolecular, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- PotentialMasterListMolecular.NeighborListAgentSourceMolecular - Class in etomica.nbr.list.molecule
-
- PotentialMasterListThreaded - Class in etomica.threaded.atom
-
- PotentialMasterListThreaded(ISimulation, ISpace) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, ISpace, double) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, ISpace, double, IAtomPositionDefinition) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, ISpace, double, BoxAgentSourceCellManagerList) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, ISpace, double, BoxAgentSourceCellManagerList, BoxAgentManager) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded - Class in etomica.threaded.domain
-
- PotentialMasterListThreaded(ISimulation, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, double, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, double, BoxAgentSourceCellManagerList, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(ISimulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<NeighborCellManager>, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded.NeighborListAgentSourceThreaded - Class in etomica.threaded.domain
-
- PotentialMasterListWorker - Class in etomica.threaded.atom
-
- PotentialMasterListWorker(int, AtomTypeAgentManager, PotentialMasterListThreaded) - Constructor for class etomica.threaded.atom.PotentialMasterListWorker
-
- PotentialMasterListWorker - Class in etomica.threaded.domain
-
- PotentialMasterListWorker(int, AtomTypeAgentManager, PotentialMasterListThreaded) - Constructor for class etomica.threaded.domain.PotentialMasterListWorker
-
- potentialMasterLong - Variable in class etomica.liquidLJ.LjMd3D
-
- potentialMasterLongCut - Variable in class etomica.liquidLJ.LjMd3D
-
- PotentialMasterLrc - Class in etomica.potential
-
Collects potentials used for long-range correction.
- PotentialMasterLrc() - Constructor for class etomica.potential.PotentialMasterLrc
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimBennet
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimTargetUmbrella
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimUmbrella
-
- PotentialMasterMonatomic - Class in etomica.potential
-
PotentialMaster suitable for monatomic molecules without using neighbor
lists and avoids PotentialMaster's performance problems.
- PotentialMasterMonatomic(ISimulation) - Constructor for class etomica.potential.PotentialMasterMonatomic
-
- PotentialMasterNbr - Class in etomica.nbr
-
- PotentialMasterNbr(ISimulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>) - Constructor for class etomica.nbr.PotentialMasterNbr
-
- PotentialMasterNbrMolecular - Class in etomica.nbr.molecule
-
- PotentialMasterNbrMolecular(ISimulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>) - Constructor for class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- potentialMasterRef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- potentialMasterRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- PotentialMasterSite - Class in etomica.nbr.site
-
- PotentialMasterSite(ISimulation, int, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
Invokes superclass constructor, specifying IteratorFactoryCell
for generating molecule iterators.
- PotentialMasterSite(ISimulation, BoxAgentManager.BoxAgentSource<BoxCellManager>, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
- PotentialMasterSite(ISimulation, BoxAgentManager.BoxAgentSource<BoxCellManager>, BoxAgentManager<BoxCellManager>, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
- PotentialMasterSite(ISimulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>, AtomsetIteratorPDT) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
- PotentialMasterSite.BoxAgentSiteSource - Class in etomica.nbr.site
-
- potentialMasterTarg - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- potentialMasterTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- potentialMasterTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- potentialMasterTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlap
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- potentialMCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- PotentialMEAM - Class in etomica.meam
-
- PotentialMEAM(ISpace) - Constructor for class etomica.meam.PotentialMEAM
-
- potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialMM - Variable in class etomica.zeolite.ZeoliteSimulation
-
The hard-sphere potential governing the interactions.
- potentialMNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialMO - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- PotentialMolecular - Class in etomica.potential
-
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.
- PotentialMolecular(int, ISpace) - Constructor for class etomica.potential.PotentialMolecular
-
General constructor for a potential instance
- potentialMolecularInterNonBondedUnlike - Variable in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- PotentialMolecularMonatomic - Class in etomica.potential
-
Intermolecular potential that wraps an atomic potential.
- PotentialMolecularMonatomic(ISpace, IPotentialAtomic) - Constructor for class etomica.potential.PotentialMolecularMonatomic
-
- PotentialMolecularSoft - Interface in etomica.potential
-
Methods for properties obtained for a soft, differentiable pair potential.
- PotentialMolecularSum - Class in etomica.potential
-
Molecular potential class that simply sums up contributions from multiple
(molecular) potentials.
- PotentialMolecularSum(IPotentialMolecular[]) - Constructor for class etomica.potential.PotentialMolecularSum
-
- potentialN - Variable in class etomica.meam.EFSTungsten
-
- potentialN - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- potentialN - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- potentialN - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- potentialN - Variable in class etomica.meam.MEAM_MC
-
- potentialN - Variable in class etomica.meam.MEAMMd3D
-
- PotentialN - Class in etomica.potential
-
- PotentialN(ISpace) - Constructor for class etomica.potential.PotentialN
-
Constructor for PotentialN.
- potentialN - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- potentialNN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialNN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialNO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialNO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- PotentialNonAdditive - Class in etomica.virial
-
Potential class which computes non-additive energies from potentials
that return the full energies for various-sized groups of molecules.
- PotentialNonAdditive(IPotentialMolecular[]) - Constructor for class etomica.virial.PotentialNonAdditive
-
- PotentialNonAdditive(IPotentialMolecular[], int[]) - Constructor for class etomica.virial.PotentialNonAdditive
-
- PotentialNonAdditive.PotentialNonAdditiveNB - Class in etomica.virial
-
- PotentialNonAdditiveNB(int) - Constructor for class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- potentialOHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialOHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialOO - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialOO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialOO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialOS - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialPlus - Variable in class etomica.virial.MayerSphericalPlus
-
- PotentialPolarizable - Interface in etomica.potential
-
Interface for a polarizable potential.
- potentialQClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQHCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQHNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- PotentialReactive - Interface in etomica.potential
-
Interface for potentials that change the bond state of an atom.
- PotentialReactive.BondChangeData - Class in etomica.potential
-
- potentialRef - Variable in class etomica.virial.MayerPTAtt
-
- potentialRef - Variable in class etomica.virial.MayerSphericalPTAtt
-
- potentials - Variable in class etomica.virial.PotentialNonAdditive
-
- potentialsAndIterators - Variable in class etomica.chem.models.Model
-
- PotentialSoft - Interface in etomica.potential
-
Methods for properties obtained for a soft, differentiable pair potential.
- potentialSpecies - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potentialSpecies - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- potentialSW - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialSW - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialSW - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
- potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialThreaded - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- potentialThreaded - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- potentialThreaded - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- PotentialThreaded - Class in etomica.threaded
-
- PotentialThreaded(ISpace, IPotentialAtomic[]) - Constructor for class etomica.threaded.PotentialThreaded
-
- PotentialTruncated - Interface in etomica.potential
-
Interface for a potential that is artificially truncated, and thus which can
provide a zero-body potential that (approximately) corrects for the
truncation.
- potentialwall - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwall1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousA - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousA1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousB - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousB1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialWater - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialWrapper - Variable in class etomica.modules.colloid.ColloidSim
-
- potentialWrapper - Variable in class etomica.modules.insertion.Insertion
-
- potentialWrapper - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- potentialWrapper - Variable in class etomica.modules.swmd.Swmd
-
- potentot(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- potentot(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- potparts(int, int, double, int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- potparts_old(int, int, double, int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- pots(double, double, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- pow - Variable in class etomica.data.DataPumpListenerPow
-
- pow - Variable in class etomica.data.DataPumpListenerPowStrict
-
- Pow - Class in etomica.graph.operations
-
- Pow() - Constructor for class etomica.graph.operations.Pow
-
- pow(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Power function.
- pow(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Raise to a positive power.
- pow(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Exponentiation with a positive integer.
- pow(int) - Method in class etomica.veos.bigdecimal.Rational
-
Power to an integer.
- pow(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Power to an integer.
- pow(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Raise to a rational power.
- pow - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- powerD(int) - Method in interface etomica.space.ISpace
-
Returns the given value raised to the Dth power, where D is the dimension of the space.
- powerD(double) - Method in interface etomica.space.ISpace
-
Returns the given value raised to the Dth power, where D is the dimension of the space.
- powerD(int) - Method in class etomica.space.Space
-
- powerD(double) - Method in class etomica.space.Space
-
- powerD(int) - Method in class etomica.space1d.Space1D
-
- powerD(double) - Method in class etomica.space1d.Space1D
-
- powerD(int) - Method in class etomica.space2d.Space2D
-
- powerD(double) - Method in class etomica.space2d.Space2D
-
- powerD(int) - Method in class etomica.space3d.Space3D
-
- powerD(double) - Method in class etomica.space3d.Space3D
-
- PowParameters - Class in etomica.graph.operations
-
- PowParameters(byte) - Constructor for class etomica.graph.operations.PowParameters
-
- powRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Raise to an integer power and round.
- powRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Raise to an integer power and round.
- powRound(BigDecimal, Rational) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Raise to a fractional power and round.
- pPade - Variable in class etomica.util.numerical.VirialOptimizer
-
- PREC - Static variable in class etomica.math.Gamma
-
- prec2err(double, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Convert a precision (relative error) to an absolute error.
- precalcQ - Variable in class etomica.virial.ClusterSumHS
-
- precalcQ - Variable in class etomica.virial.ClusterWheatleyHS
-
- precalcQ - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- precision - Variable in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- precision - Variable in class etomica.graphics.DeviceBox
-
Integer specifying the number of significant figures to be displayed.
- precision - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- precision_s - Variable in class etomica.potential.EwaldSumMolecules
-
- precisionLimit - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- PreconditionedConjugateGradient - Class in etomica.conjugategradient
-
- PreconditionedConjugateGradient(Matrix, Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.PreconditionedConjugateGradient
-
- PreconditionedConjugateGradientAlgorithm() - Method in class etomica.conjugategradient.PreconditionedConjugateGradient
-
Preconditioned Conjugate Gradient solution for
Ax = b
- predefinedArgbs - Static variable in class org.jmol.util.Colix
-
- predefinedGroup1Names - Static variable in class org.jmol.viewer.JmolConstants
-
- predefinedGroup3Names - Static variable in class org.jmol.viewer.JmolConstants
-
- predefinedStatic - Static variable in class org.jmol.viewer.JmolConstants
-
- predefinedVariable - Static variable in class org.jmol.viewer.JmolConstants
-
- predictor() - Method in class etomica.integrator.IntegratorGear4
-
- predictor() - Method in class etomica.integrator.IntegratorGear4NPH
-
- Prefix - Class in etomica.units
-
Base class for all unit prefixes, such as kilo, micro, nano, etc.
- prefix() - Method in class etomica.units.PrefixedUnit
-
Returns the prefix of the baseUnit.
- prefixAllowed() - Method in class etomica.units.CompoundUnit
-
- prefixAllowed() - Method in class etomica.units.PrefixedUnit
-
Returns false to indicate that a prefix cannot be applied to an already
prefixed baseUnit.
- prefixAllowed() - Method in class etomica.units.SimpleUnit
-
Returns flag indicating whether a prefix is allowed with this unit.
- prefixAllowed() - Method in class etomica.units.systems.LJ.LJUnit
-
- prefixAllowed() - Method in interface etomica.units.Unit
-
Indicates if the unit is appropriate for use with a prefix.
- PrefixedUnit - Class in etomica.units
-
Implementation of the Unit interface formed from a base Unit (e.
- PrefixedUnit(Unit) - Constructor for class etomica.units.PrefixedUnit
-
Constructs a PrefixedUnit using the given base and a Null prefix
- PrefixedUnit(Prefix, Unit) - Constructor for class etomica.units.PrefixedUnit
-
Constructs a PrefixedUnit using the given prefix and base
- preMultiply(Quaternion) - Method in class etomica.math.Quaternion
-
Returns the Quaternion r resulting from multiplying the input Quaternion preMultiplier to the current Quaternion q.
- pRes - Variable in class etomica.normalmode.MeterSolidDA
-
- preservestate - Static variable in class org.jmol.script.Token
-
- press() - Method in class etomica.graphics.DeviceButton
-
Performs the button's action.
- press() - Method in class etomica.zeolite.DeviceButtonSingle
-
Performs the button's action.
- pressure - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- pressure - Variable in class etomica.association.MCMoveVolumeAssociated
-
- pressure - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- pressure - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.data.meter.MeterWidomInsertion
-
- pressure - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- pressure - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- pressure - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- pressure - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- pressure - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
-
- pressure - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- pressure(double) - Method in class etomica.modules.adsorption.EOSSW
-
- pressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- pressure - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- pressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- pressure - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- pressure - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- pressure - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- pressure - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- pressure - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- pressure - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- pressure - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- pressure - Variable in class etomica.statmech.HardSphereSolid.EOSParams
-
- Pressure - Class in etomica.units
-
Dimension for (3D) pressure.
- pressure() - Method in class etomica.units.systems.CGS
-
- pressure() - Method in class etomica.units.systems.LJ
-
- pressure() - Method in class etomica.units.systems.MKS
-
- pressure() - Method in class etomica.units.systems.UnitSystem
-
- pressure() - Method in class etomica.units.systems.UnitSystem.Sim
-
- pressure - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- pressure0 - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- Pressure2D - Class in etomica.units
-
Simulation unit of (2D) pressure is (D-A/ps^2)/A = D/ps^2
- pressure2D() - Method in class etomica.units.systems.UnitSystem.Sim
-
- pressureAverage - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- pressureDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureFast - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- pressureFull - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- pressureHistory - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- pressureMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureSliderPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureTensor - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
- pressureTensor - Variable in class etomica.integrator.IntegratorRigidIterative
-
- pressureTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- pressureTensor - Variable in class etomica.integrator.IntegratorVelocityVerlet
-
- pressureTensor - Variable in class etomica.integrator.IntegratorVerlet
-
- pressureTensor - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- pressureTensor - Variable in class etomica.potential.PotentialCalculationForcePressureSum
-
- pressureTensor - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- pressureTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- pretendBox - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- pretendBox - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- pretendBox - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- pretendBox - Variable in class etomica.normalmode.MeterDDP
-
- pretendBox - Variable in class etomica.normalmode.MeterDP
-
- pretendBox - Variable in class etomica.normalmode.MeterTargetTP
-
- prev - Variable in class etomica.lattice.IndexIteratorIncreasing
-
- prev - Static variable in class org.jmol.script.Token
-
- previous - Variable in class etomica.util.FunctionChain.Link
-
- previous - Variable in class etomica.util.TreeLinker
-
- previousTensor - Variable in class etomica.models.water.OrientationCalcWater3P
-
- previousTensor - Variable in class etomica.models.water.OrientationCalcWater4P
-
- previousValue - Variable in class etomica.normalmode.ModifierCells3D
-
- previousValue - Variable in class etomica.normalmode.ModifierXCells2D
-
- previousValue - Variable in class etomica.normalmode.ModifierYCells2D
-
- prevprime(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
return the largest prime smaller than n
- pRigid - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- primaryCoordDef - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- primaryCoordDef - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- Prime - Class in etomica.veos.bigdecimal
-
Prime numbers.
- Prime() - Constructor for class etomica.veos.bigdecimal.Prime
-
Default constructor initializing a list of primes up to 17.
- primeexp - Variable in class etomica.veos.bigdecimal.Ifactor
-
- primitive - Variable in class etomica.lattice.BravaisLattice
-
- Primitive - Class in etomica.lattice.crystal
-
Collection of primitive elements that specify or are determined
by the structure of a Bravais lattice.
- Primitive(ISpace) - Constructor for class etomica.lattice.crystal.Primitive
-
This constructor is called directly when a Primitive is constructing
its reciprocal primitive.
- primitive - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- primitive - Variable in class etomica.models.hexane.TestHexane
-
- primitive - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- primitive - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- primitive - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- primitive - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- primitive - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- primitive - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- primitive - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- primitive - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- primitive - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- primitive - Variable in class etomica.normalmode.CoordinateDefinition
-
- primitive - Variable in class etomica.normalmode.HessianDB
-
- primitive - Variable in class etomica.normalmode.LJVacancyMin
-
- primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- primitive - Variable in class etomica.normalmode.NormalModes2D
-
- primitive - Variable in class etomica.normalmode.NormalModes3D
-
- primitive - Variable in class etomica.normalmode.NormalModesMolecular
-
- primitive - Variable in class etomica.normalmode.SimBennet
-
- primitive - Variable in class etomica.normalmode.SimCalcJ
-
- primitive - Variable in class etomica.normalmode.SimCalcS
-
- primitive - Variable in class etomica.normalmode.SimCalcSLJ
-
- primitive - Variable in class etomica.normalmode.SimCalcSMorse
-
- primitive - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- primitive - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- primitive - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- primitive - Variable in class etomica.normalmode.SimEinStep1
-
- primitive - Variable in class etomica.normalmode.SimEinStep1HCP
-
- primitive - Variable in class etomica.normalmode.SimEinStep2
-
- primitive - Variable in class etomica.normalmode.SimEinStep2HCP
-
- primitive - Variable in class etomica.normalmode.SimHarmonic
-
- primitive - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- primitive - Variable in class etomica.normalmode.SimLJHTTISuper
-
- primitive - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- primitive - Variable in class etomica.normalmode.SimModesJ
-
- primitive - Variable in class etomica.normalmode.SimOverlap
-
- primitive - Variable in class etomica.normalmode.SimOverlapLJ
-
- primitive - Variable in class etomica.normalmode.SimOverlapLJModule
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- primitive - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- primitive - Variable in class etomica.normalmode.SimTarget
-
- primitive - Variable in class etomica.normalmode.SimTargetUmbrella
-
- primitive - Variable in class etomica.normalmode.SimUmbrella
-
- primitive - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- primitive - Variable in class etomica.normalmode.WaveVectorFactory2D
-
- primitive - Variable in class etomica.normalmode.WaveVectorFactoryFcc
-
- primitive - Variable in class etomica.normalmode.WaveVectorFactorySimple
-
- primitive - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- primitive - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- primitive - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- PrimitiveBcc - Class in etomica.lattice.crystal
-
Primitive group for a body-centered-cubic system.
- PrimitiveBcc(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveBcc
-
- PrimitiveBcc(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveBcc
-
- PrimitiveCubic - Class in etomica.lattice.crystal
-
Primitive group for a cubic system.
- PrimitiveCubic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveCubic
-
- PrimitiveCubic(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveCubic
-
- PrimitiveFcc - Class in etomica.lattice.crystal
-
Primitive group for a face-centered-cubic system.
- PrimitiveFcc(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveFcc
-
- PrimitiveFcc(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveFcc
-
- PrimitiveGeneral - Class in etomica.lattice.crystal
-
Primitive defined simply by its vectors.
- PrimitiveGeneral(ISpace, IVector[]) - Constructor for class etomica.lattice.crystal.PrimitiveGeneral
-
- PrimitiveHexagonal - Class in etomica.lattice.crystal
-
Primitive group for a hexagonal system.
- PrimitiveHexagonal(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal
-
- PrimitiveHexagonal(ISpace, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal
-
- PrimitiveHexagonal.PrimitiveHexagonalReciprocal - Class in etomica.lattice.crystal
-
- PrimitiveHexagonal2D - Class in etomica.lattice.crystal
-
Primitive group for a 2D hexagonal system.
- PrimitiveHexagonal2D(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- PrimitiveHexagonal2D(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal - Class in etomica.lattice.crystal
-
- PrimitiveHexagonal2DReciprocal(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
-
- PrimitiveHexagonalReciprocal(ISpace, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal.PrimitiveHexagonalReciprocal
-
- PrimitiveHexane - Class in etomica.models.hexane
-
Implements the triclinic crystal structure derived from Dr.
- PrimitiveHexane(ISpace) - Constructor for class etomica.models.hexane.PrimitiveHexane
-
- PrimitiveMonoclinic - Class in etomica.lattice.crystal
-
Primitive group for a monoclinic system.
- PrimitiveMonoclinic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic
-
- PrimitiveMonoclinic(ISpace, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic
-
- PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal - Class in etomica.lattice.crystal
-
- PrimitiveMonoclinicReciprocal(ISpace, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
-
- PrimitiveOrthorhombic - Class in etomica.lattice.crystal
-
Primitive group for an orthorhombic system.
- PrimitiveOrthorhombic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- PrimitiveOrthorhombic(ISpace, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- PrimitiveOrthorhombicHexagonal - Class in etomica.lattice.crystal
-
Primitive group for an orthorhombic system.
- PrimitiveOrthorhombicHexagonal(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- PrimitiveTetragonal - Class in etomica.lattice.crystal
-
Primitive group for a tetragonal system.
- PrimitiveTetragonal(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveTetragonal
-
- PrimitiveTetragonal(ISpace, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTetragonal
-
- PrimitiveTriclinic - Class in etomica.lattice.crystal
-
Primitive group for a triclinic system.
- PrimitiveTriclinic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveTriclinic
-
- PrimitiveTriclinic(ISpace, double, double, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTriclinic
-
- PrimitiveTrigonal - Class in etomica.lattice.crystal
-
Primitive group for a trigonal system.
- PrimitiveTrigonal(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveTrigonal
-
- PrimitiveTrigonal(ISpace, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTrigonal
-
- primitiveUnitCell - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- primitiveUnitCell - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- primitiveUnitCell - Variable in class etomica.normalmode.HessianDB
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimCalcSLJ
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapLJ
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- print(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
-
- print - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- print - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- print - Variable in class etomica.potential.P2HydrogenPatkowski
-
- print - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- print() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
-
- printapalooza - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- printInConvertedUnits - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- printInterval - Variable in class etomica.integrator.IntegratorRigidIterative
-
- printInterval - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- printInterval - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- printInterval - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- printKeyAtomPositions() - Method in class etomica.action.IntegratorDimerApproach
-
- printResults(double) - Method in class etomica.virial.simulations.SimulationVirial
-
- printResults(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- printResults(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- printResults(double, String[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- printStrands(List, int) - Static method in class etomica.graph.property.FFTDecomposition
-
- printStrands(List, int) - Static method in class etomica.graph.property.IsFFT
-
- printStrands(List, int) - Static method in class etomica.virial.CalcFFT
-
- printTargetHistogram() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Prints out the target histogram of maximum separation distances as
set up by setupTargetHistogram().
- probabilityBins - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- probabilityBins - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- probabilityReverseMap - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- probabilityReverseMap - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- probe - Static variable in class org.jmol.script.Token
-
- proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer got an error while
transcoding the input source.
- proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in class etomica.graph.view.rasterizer.Main
-
- proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer got an error while
transcoding the input source.
- proceedWithComputedTask(Transcoder, Map, List, List) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer has computed the
exact description of what it should do.
- proceedWithComputedTask(Transcoder, Map, List, List) - Method in class etomica.graph.view.rasterizer.Main
-
- proceedWithComputedTask(Transcoder, Map, List, List) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer has computed the
exact description of what it should do.
- proceedWithSourceTranscoding(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer is about to start transcoding
of a given source.
- proceedWithSourceTranscoding(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.Main
-
- proceedWithSourceTranscoding(SVGConverterSource, File) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer is about to start transcoding
of a given source.
- processAtoms(IAtomList) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- processData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- processData(IData) - Method in class etomica.data.DataAccumulator
-
Implementation of DataProcessor interface.
- processData(IData) - Method in class etomica.data.DataGroupFilter
-
Returns the output data that was established with a previous call to
processDataInfo.
- processData(IData) - Method in class etomica.data.DataHistogram
-
Adds each value in the given Data to a single histogram.
- processData(IData) - Method in class etomica.data.DataLogger
-
Gives data to DataSink for writing
- processData(IData) - Method in class etomica.data.DataProcessor
-
Processes the input Data and returns Data for pushing to the next
DataSink.
- processData(IData) - Method in class etomica.data.DataProcessorChemicalPotential
-
- processData(IData) - Method in class etomica.data.DataProcessorFunction
-
Applies the function to all elements of the input data.
- processData(IData) - Method in class etomica.data.DataProcessorInterfacialTension
-
- processData(IData) - Method in class etomica.data.DataPump
-
Returns the given Data.
- processData(IData) - Method in class etomica.data.types.CastGroupOfTablesToDataTable
-
Converts data in given group to a DataDoubleArray as described in the
general comments for this class.
- processData(IData) - Method in class etomica.data.types.CastGroupToDoubleArray
-
Converts data in given group to a DataDoubleArray as described in the
general comments for this class.
- processData(IData) - Method in class etomica.data.types.CastToDouble
-
Extracts a double from the input data and returns it encapsulated in a
DataDouble.
- processData(IData) - Method in class etomica.data.types.CastToDoubleArray
-
Copies input Data to a DataDoubleArray and returns it (the DataDataDoubleArray).
- processData(IData) - Method in class etomica.data.types.CastToGroup
-
Processes the input Data to update the output DataGroup.
- processData(IData) - Method in class etomica.data.types.CastToTable
-
Copies input Data to a DataTable and returns it (the DataTable).
- processData(IData) - Method in class etomica.densityofstate.DataProcessorPhi
-
- processData(IData) - Method in class etomica.liquidLJ.DataProcessorReweight
-
- processData(IData) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
-
- processData(IData) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- processData(IData) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- processData(IData) - Method in class etomica.meam.DataProcessorCvMD
-
- processData(IData) - Method in class etomica.metastable.DataProcessorXY
-
- processData(IData) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
-
- processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- processData(IData) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
-
- processData(IData) - Method in class etomica.modules.entropylottery.EntropyProcessor
-
- processData(IData) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- processData(IData) - Method in class etomica.modules.interfacial.FitTanh
-
- processData(IData) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
-
- processData(IData) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
-
- processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBias
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorVar
-
- processData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
-
- processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- processData(IData) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.normalmode.BoltzmannProcessor
-
- processData(IData) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- processData(IData) - Method in class etomica.normalmode.DataProcessorSum
-
- processData(IData) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
-
- processData(IData) - Method in class etomica.surfacetension.FitTanh
-
- processData(IData) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- processData(IData) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
take in v1/pi1, pi0/pi1, spit out v1/pi, overlap0, overlap1, overlap2...
- processData(IData) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
-
- processData(IData) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverage
-
Prepares the accumulator for input data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlockless
-
Prepares the accumulator for input data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageCovariance
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixed
-
Prepares the accumulator for input data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Prepares the accumulator for input data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorCounter
-
Does nothing.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorHistogram
-
Sets up data and histograms, discarding any previous results.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorHistory
-
Sets up data and histories, discarding any previous results.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorRatioAverage
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorRatioAverageCovariance
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataGroupFilter
-
Determines data that will be output, using the given DataInfo and
the index specification given at construction.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataHistogram
-
Sets up the histogram, discarding any previous results.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataLogger
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessor
-
Informs this DataProcessor of the DataInfo for the Data it will be
processing.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorChemicalPotential
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorFunction
-
Returns a copy of the given dataInfo
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorInterfacialTension
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataPump
-
Returns the given DataInfo.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastGroupOfTablesToDataTable
-
Prepares processor to handle Data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastGroupToDoubleArray
-
Prepares processor to handle Data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToDouble
-
Prepares processor to handle Data.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToDoubleArray
-
Prepares processor to perform cast.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToGroup
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToTable
-
Prepares processor to perform cast.
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.densityofstate.DataProcessorPhi
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweight
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.meam.DataProcessorCvMD
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.metastable.DataProcessorXY
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.entropylottery.EntropyProcessor
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.FitTanh
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBias
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorVar
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.normalmode.BoltzmannProcessor
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.normalmode.DataProcessorSum
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.surfacetension.FitTanh
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
-
- processDataInfo(IEtomicaDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
-
- processReverseList() - Method in class etomica.integrator.IntegratorHard
-
Recalculate collision times (up) for any atoms atoms in the "reverse"
list of atoms that thought they would collide with an atom that's
changed.
- product(ClusterDiagram, ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns a new cluster that is the product of the given clusters.
- product(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns the product of all the given clusters.
- product(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns an array of clusters formed from taking the product of each of the diagrams
of the first set with each of the diagrams of the second set.
- product(int[]) - Static method in class etomica.virial.cluster.Standard
-
Prepares a set of bond pairs for a clusters
formed from a disconnected set of fully connected subclusters.
- product3D(IVectorMutable, IVector, IVector) - Method in class etomica.potential.P2SpheroPolyhedron
-
- profile1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profile1pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profile2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profile2pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profileData - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- profileDataInfo - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- profileDim - Variable in class etomica.data.meter.MeterProfile
-
Vector describing the orientation of the profile.
- profileDim - Variable in class etomica.data.meter.MeterProfileByAtoms
-
Vector describing the orientation of the profile.
- profileDim - Variable in class etomica.data.meter.MeterProfileByVolume
-
Vector describing the orientation of the profile.
- profileDim - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- profilePlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- proj - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- proja - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- projb - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- projectOntoAxis(Point3f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- prompt(String, String, String[], boolean) - Method in interface org.jmol.api.ApiPlatform
-
- prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
-
- prop - Variable in class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
-
- property - Variable in class etomica.graph.operations.SetPropertyFilter
-
- Property - Interface in etomica.graph.property
-
- property - Variable in class etomica.graphics.DeviceSlider
-
Property being modulated
- property - Variable in class etomica.graphics.DeviceSpinner
-
Property being modulated
- property - Variable in class etomica.modifier.ModifierGeneral
-
- property - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- property - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- property - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- property - Static variable in class org.jmol.script.Token
-
- PROPERTY_ALL - Static variable in class etomica.graph.operations.MaxIsomorph
-
- propertyatomnumbercolumncount - Static variable in class org.jmol.script.Token
-
- propertyatomnumberfield - Static variable in class org.jmol.script.Token
-
- propertyChange(PropertyChangeEvent) - Method in class etomica.graphics.PropertyText
-
Listen to update display if editor changes value in some other way.
- propertyChange(PropertyChangeEvent) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
Called when a field's "value" property changes.
- propertycolorscheme - Static variable in class org.jmol.script.Token
-
- propertydatacolumncount - Static variable in class org.jmol.script.Token
-
- propertydatafield - Static variable in class org.jmol.script.Token
-
- PropertyFilter - Class in etomica.graph.iterators.filters
-
- PropertyFilter(GraphIterator, Property) - Constructor for class etomica.graph.iterators.filters.PropertyFilter
-
- propertyFilter - Variable in class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
-
- PROPERTYFLAGS - Static variable in class org.jmol.script.Token
-
- PropertyImpl - Class in etomica.graph.engine.impl
-
- PropertyImpl(String) - Constructor for class etomica.graph.engine.impl.PropertyImpl
-
- PropertyText - Class in etomica.graphics
-
- PropertyText(PropertyEditor) - Constructor for class etomica.graphics.PropertyText
-
- pRotConstraint - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- PRotConstraint - Class in etomica.models.nitrogen
-
- PRotConstraint(ISpace, CoordinateDefinitionNitrogen, IBox) - Constructor for class etomica.models.nitrogen.PRotConstraint
-
- pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- protein - Static variable in class org.jmol.script.Token
-
- Psat - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- pSat() - Method in class etomica.modules.adsorption.EOSSW
-
- psi(double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Digamma function.
- psi - Static variable in class org.jmol.script.Token
-
- pSimData - Variable in class etomica.util.numerical.B9Optimizer
-
- pSimData - Variable in class etomica.util.numerical.VirialOptimizer
-
- pSoluteMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- pSolutePM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- pSolutePP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- pSpan - Variable in class etomica.normalmode.MeterDDP
-
- pSpan - Variable in class etomica.normalmode.MeterDP
-
- pSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- pSplitter - Variable in class etomica.normalmode.DataSourceAvgPressure
-
- pSplitter - Variable in class etomica.normalmode.DataSourceAvgPressure2
-
- pSplitter - Variable in class etomica.normalmode.DataSourceMuRoot
-
- pSplitter - Variable in class etomica.normalmode.DataSourceMuRoot1
-
- pSplitter - Variable in class etomica.normalmode.DataSourceMuRootPMatch
-
- pSplitter - Variable in class etomica.normalmode.DataSourcePMu
-
- pSplitter - Variable in class etomica.normalmode.DataSourcePN
-
- psuedoSinks - Variable in class etomica.data.DataSet
-
- pSum - Variable in class etomica.normalmode.HSNPT.MyAgent
-
- pSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pSum2 - Variable in class etomica.normalmode.HSNPT.MyAgent
-
- pSumXYZ - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pSumXYZ1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- pSumXYZ1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pSumXYZ2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- pSumXYZ2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pt - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- pt - Variable in enum org.jmol.constant.EnumVdw
-
- pt4Value(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- pThermalize - Variable in class etomica.modules.adsorption.P1Wall
-
- pTmp - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pTmp1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- pTmp1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pTmp2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- pTmp2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pTruncated - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- pTruncatedAA - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- pTruncatedAB - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- ptValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- pTW - Variable in class etomica.interfacial.LJMC
-
- pTW - Variable in class etomica.interfacial.LJMD
-
- pType - Variable in class etomica.models.nitrogen.SpeciesN2
-
- pType - Variable in class etomica.models.nitrogen.SpeciesN2B
-
- pType - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- pU - Variable in class etomica.virial.MayerENonGeneral
-
- pullFactor - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- pump - Variable in class etomica.simulation.prototypes.LjMd3D
-
- pump - Variable in class etomica.spin.Heisenberg
-
- pump - Variable in class etomica.thermointegration.LjMc3D
-
- pUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- pUnit - Variable in class etomica.modules.swmd.SwmdGraphic
-
- purine - Static variable in class org.jmol.script.Token
-
- PURPLE - Static variable in class org.jmol.util.Colix
-
- pushInterval - Variable in class etomica.data.DataAccumulator
-
Accumulated data are pushed to the data sinks after every pushInterval calls
- pushme - Static variable in class etomica.virial.ClusterWheatleySoft
-
- pushme - Static variable in class etomica.virial.ClusterWheatleySoftBD
-
- pushR2 - Variable in class etomica.virial.ClusterSumMultibody
-
- pushR2 - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizable
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- put(int, int) - Method in class org.jmol.util.Int2IntHash
-
- put_rigid() - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- putCount - Variable in class etomica.data.DataAccumulator
-
Counter that keeps track of the number of interval events received since last call to updateSums
- putData(IData) - Method in class etomica.data.DataArrayWriter
-
- putData(IData) - Method in class etomica.data.DataDistributer
-
- putData(IData) - Method in class etomica.data.DataDump
-
- putData(IData) - Method in class etomica.data.DataFork
-
Puts the given Data through into all DataSinks.
- putData(IData) - Method in class etomica.data.DataGroupSplitter
-
- putData(IData) - Method in class etomica.data.DataLogger
-
Performs the open/write/close file actions in accordance with the
settings of the Logger.
- putData(IData) - Method in class etomica.data.DataProcessor
-
Processes input Data and pushes it downstream if output Data and DataSink
are not null.
- putData(IData) - Method in class etomica.data.DataSet.DataSetSink
-
- putData(IData) - Method in class etomica.data.DataSinkConsole
-
Causes the given values to be written to the print stream.
- putData(IData) - Method in class etomica.data.DataSplitter
-
- putData(IData) - Method in class etomica.data.DataTableWriter
-
- putData(IData) - Method in interface etomica.data.IDataSink
-
Gives data to DataSink for processing, display, or whatever it does.
- putData(IData) - Method in class etomica.graphics.DisplayTextBox
-
Sets the display text to reflect the desired value from the datasource.
- putData(IData) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- putData(IData) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Add the given values to the sums and block sums
- putData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
Prepares the accumulator for input data.
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixed
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataArrayWriter
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataDistributer
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataDump
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataFork
-
Puts the given DataInfo through into all DataSinks, inserting
a data caster before any sinks needing one.
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataGroupSplitter
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessor
-
Invokes processDataInfo on the given DataInfo, and passes the returned
DataInfo to the dataSink (if not null).
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataSet.DataSetSink
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataSinkConsole
-
Causes the given DataInfo to be written to the print stream.
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataSplitter
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataTableWriter
-
- putDataInfo(IEtomicaDataInfo) - Method in interface etomica.data.IDataSink
-
Informs the DataSink of the type of Data it should expect to receive.
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayTextBox
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- putDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- putEdge(byte) - Method in interface etomica.graph.model.Graph
-
- putEdge(byte, byte) - Method in interface etomica.graph.model.Graph
-
- putEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- putEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- putValue(String, Object) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- pvBox - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- pVirial - Variable in class etomica.util.numerical.B9Optimizer
-
- pWater - Variable in class etomica.dielectric.TIP4P_NVT
-
- pWertheim2Site - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- Pwr2 - Static variable in class org.jmol.util.TriangleData
-
- PY - Static variable in class etomica.virial.cluster.ClusterOperations
-
- PYGenerate(int, char) - Static method in class etomica.virial.PYGenerator
-
Returns the graphs (at each order, up to n+2) in the PY approximation to c.
- PYGenerator - Class in etomica.virial
-
- PYGenerator() - Constructor for class etomica.virial.PYGenerator
-
- PYGenerator.IteratorEF - Class in etomica.virial
-
- pyrimidine - Static variable in class org.jmol.script.Token
-
- pythag(double, double) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
-
- r - Variable in class etomica.action.IntegratorDimerApproach
-
- r - Variable in class etomica.association.MCMoveVolumeAssociated
-
- r - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- R - Variable in class etomica.conjugategradient.ConjugateGradients
-
- R - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- R - Variable in class etomica.conjugategradient.SteepestDescent
-
- r - Variable in class etomica.modules.rheology.ConformationPolymer
-
- r - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- r - Variable in class etomica.modules.sam.P1Sinusoidal
-
- r0 - Variable in class etomica.association.MCMoveDimerRotate
-
- r0 - Variable in class etomica.association.MCMoveSmerRotate
-
- r0 - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- r0 - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- r0 - Variable in class etomica.meam.ParameterSetMEAM
-
- r0 - Variable in class etomica.meam.PotentialCuLREP
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- R0 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- R0 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- R0 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- R0 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- r0 - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
-
- r0 - Static variable in class etomica.potential.P2HydrogenHindePatkowski
-
- r0 - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- r0 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- R0 - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
-
- r0 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r0 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r00 - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- r01Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r01Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r02Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r02Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- R1 - Variable in class etomica.meam.PotentialFeEAM_LS
-
- R1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- R1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- R1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- r1 - Variable in class etomica.potential.P3HydrogenATM
-
- r1 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r1 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r12 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- r12 - Variable in class etomica.potential.P3QChem.DampingParams
-
- r12Vec - Variable in class etomica.potential.PotentialEmul
-
- r12Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r12Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- R2 - Variable in class etomica.meam.PotentialFeEAM_LS
-
- r2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- r2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- r2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- r2 - Variable in class etomica.nbr.CriterionSimple
-
- r2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- r2 - Variable in class etomica.potential.P3HydrogenATM
-
- r2(Vector1D, Vector1D, IBoundary) - Static method in class etomica.space1d.Space1D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector1D, Vector1D, IBoundary, Vector1D) - Static method in class etomica.space1d.Space1D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector2D, Vector2D, IBoundary) - Static method in class etomica.space2d.Space2D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector2D, Vector2D, IBoundary, Vector2D) - Static method in class etomica.space2d.Space2D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector3D, Vector3D, IBoundary) - Static method in class etomica.space3d.Space3D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector3D, Vector3D, IBoundary, Vector3D) - Static method in class etomica.space3d.Space3D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2 - Variable in class etomica.virial.ClusterSumMultibody
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- r2 - Variable in class etomica.virial.CoordinatePairLeafSet
-
- r2 - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- r2 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r2 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r2a - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- r2ab - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- r2b - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- r2Core - Variable in class etomica.potential.PotentialEmul
-
- r2Cut - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- r2Cutoff - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- r2Cutoff - Variable in class etomica.potential.P2MoleculeTruncated
-
- r2Cutoff - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- r2Cutoff - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- r2Cutoff - Variable in class etomica.potential.P2SoftTruncated
-
- r2Cuts - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- r2Cuts - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- r2d2udr2 - Variable in class etomica.virial.PercusYevick1QC
-
- r2Data - Variable in class etomica.potential.P2QChemInterpolated
-
- r2MaxSafe - Variable in class etomica.nbr.CriterionSimple
-
- r2MaxSafe - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- r2Switch - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- r2Switch - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- R3 - Variable in class etomica.meam.PotentialFeEAM_LS
-
- r3 - Variable in class etomica.potential.P3HydrogenATM
-
- rAB - Variable in class etomica.potential.EwaldSummation
-
- rac - Variable in class etomica.dimer.P1LepsHarmonic
-
- rAccum - Variable in class etomica.data.meter.MeterMeanSquareDisplacement
-
- radau_f1_tst(IVectorMutable[]) - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- Radian - Class in etomica.units
-
Simulation unit for the measure of an angle.
- radiansPerDegree - Static variable in class org.jmol.util.Measure
-
- radiansPerDegree - Static variable in class org.jmol.viewer.JmolConstants
-
- radicalColorMap - Variable in class etomica.modules.catalysis.ColorSchemeRadical
-
- radicalColorMap - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- radioB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- radioB1 - Variable in class etomica.modules.clustergenerator.MyApplet
-
- radius - Variable in class etomica.math.geometry.Hypersphere
-
- radius - Static variable in class org.jmol.script.Token
-
- random - Variable in class etomica.action.AtomActionRandomizeVelocity
-
- random - Variable in class etomica.association.AtomSourceRandomDimer
-
- random - Variable in class etomica.association.AtomSourceRandomSmer
-
- random - Variable in class etomica.association.ColorSchemeSmer
-
- random - Variable in class etomica.association.ColorSchemeSmerByLength
-
- random - Variable in class etomica.association.MCMoveDimer
-
- random - Variable in class etomica.association.MCMoveDimerRotate
-
- random - Variable in class etomica.association.MCMoveSmer
-
- random - Variable in class etomica.association.MCMoveSmerRotate
-
- random - Variable in class etomica.association.MoleculeSourceRandomDimer
-
- random - Variable in class etomica.atom.AtomSourceRandomLeaf
-
- random - Variable in class etomica.atom.AtomSourceRandomSpecies
-
- random - Variable in class etomica.atom.MoleculeSourceRandomMolecule
-
- random - Variable in class etomica.box.RandomPositionSourceDeformable
-
- random - Variable in class etomica.box.RandomPositionSourceRectangular
-
- random - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- random - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- random - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- random - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- random - Variable in class etomica.integrator.IntegratorManagerMC
-
- random - Variable in class etomica.integrator.IntegratorMC
-
- random - Variable in class etomica.integrator.IntegratorMD
-
Elementary time step for the MD simulation
- random - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- random - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- random - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- random - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- random - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- random - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- random(int, int) - Static method in class etomica.math.linearalgebra.Matrix
-
- random - Variable in class etomica.models.hexane.MCMoveCBMC
-
- random - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- random - Variable in class etomica.models.hexane.MCMoveReptate
-
- random - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- random - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- random - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- random - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- random - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- random - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- random - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- random - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- random - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- random - Variable in class etomica.modules.adsorption.P1Wall
-
- random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
-
- random - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- random - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- random - Variable in class etomica.modules.droplet.ConfigurationDroplet
-
- random - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- random - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- random - Variable in class etomica.modules.rheology.ConformationPolymer
-
- random - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- random - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- random - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- random - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- random - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
-
- random - Variable in class etomica.normalmode.MCMoveHarmonic
-
- random - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- random - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- random - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- random - Variable in class etomica.normalmode.MCMoveSingleMode
-
- random - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- random - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- random - Variable in class etomica.normalmode.MCMoveWV
-
- random - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- random - Variable in class etomica.simulation.Simulation
-
- random - Variable in class etomica.spin.MCMoveSpinFlip
-
- random - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- random - Variable in class etomica.virial.cluster.ClusterDiagramTree
-
- random - Variable in class etomica.virial.ClusterSumStickyEF
-
- random - Variable in class etomica.virial.ConfigurationClusterAceticAcid
-
- random - Variable in class etomica.virial.ConfigurationClusterMove
-
- random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- random - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- random - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- random - Variable in class etomica.virial.MCMoveClusterReptateMulti
-
- random - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- random - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- random - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- random - Variable in class etomica.virial.MCMoveClusterRingScale
-
- random - Variable in class etomica.virial.MeterVirialBDBin
-
- random - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- random - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- random - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- random1 - Variable in class etomica.dimer.IntegratorDimerRT
-
- randomAtom0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- randomAtom1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- randomDirection(IRandom) - Method in class etomica.space1d.Vector1D
-
- randomizeDiagram() - Method in class etomica.virial.ClusterSumStickyEF
-
set the diagram used for calculating the value to a random one.
- randomizeMomenta() - Method in class etomica.integrator.IntegratorHard
-
Updates collision times appropriately after randomizing momenta
as part of the Andersen thermostat.
- randomizeMomenta() - Method in class etomica.integrator.IntegratorMD
-
randomizes the velocities for the given box using velocities
chosen form a Maxwell-Boltzmann distribution as in the Andersen
thermostat.
- randomizeMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
-
- randomizeMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- randomizeMomenta() - Method in class etomica.integrator.IntegratorVerlet
-
Updates MrLast appropriately after randomizing momenta
as part of the Andersen thermostat.
- randomizeMomenta() - Method in class etomica.interfacial.IntegratorFixedWall
-
- randomizeMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorHard
-
Updates collision time appropriately after randomizing momentum
as part of the Andersen thermostat.
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorMD
-
randomizes the velocity of an atom in the given box using velocities
chosen form a Maxwell-Boltzmann distribution as in the Andersen
thermostat.
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorRigidIterative
-
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorVerlet
-
Updates MrLast appropriately after randomizing momentum
as part of the Andersen thermostat.
- randomizeMomentum(IAtomKinetic) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- randomizePositions() - Method in class etomica.dimer.SimDimerLJadatom
-
- randomizePositions() - Method in class etomica.kmc.IntegratorKMC
-
- randomizePositions() - Method in class etomica.kmc.IntegratorKMCCluster
-
- randomizePositions() - Method in class etomica.kmc.SimKMCLJadatom
-
- randomizePositions() - Method in class etomica.kmc.SimKMCMEAMadatom
-
- randomizer - Variable in class etomica.modules.adsorption.P1Wall
-
- randomizeTotalKE() - Method in class etomica.integrator.IntegratorHard
-
Updates collision times appropriately after randomizing momenta
as part of the Andersen scaling thermostat.
- randomizeTotalKE() - Method in class etomica.integrator.IntegratorMD
-
- randomLensPoint(IVector, IVector, Vector3D, IVectorMutable, double) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
Sets a given vector to a point chosen uniformly at random in the lens-shaped region
formed by the overlap of two spheres of unit radius located at the given positions r1 and r2.
- randomLensPoint(double, Vector3D) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
Returns a randomly selected point from within the lens-shaped region of
overlap of two spheres of unit radius separated by a distance d.
- randomLensPointInBox(IVector, IVector, IVectorRandom) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- RandomMersenneTwister - Class in etomica.util
-
Mersenne Twister RNG.
- RandomMersenneTwister(int) - Constructor for class etomica.util.RandomMersenneTwister
-
Creates a Mersenne Twister with the given seed.
- RandomMersenneTwister(int[]) - Constructor for class etomica.util.RandomMersenneTwister
-
Creates a Mersenne Twister with the given array of seeds.
- randomMol0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- randomMol1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- randomNumber0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- randomNumber1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- RandomNumberGenerator - Class in etomica.util
-
Random number generator class.
- RandomNumberGenerator() - Constructor for class etomica.util.RandomNumberGenerator
-
- RandomNumberGenerator(long) - Constructor for class etomica.util.RandomNumberGenerator
-
- RandomNumberGeneratorUnix - Class in etomica.util
-
Random number generator that takes random bits from files.
- RandomNumberGeneratorUnix() - Constructor for class etomica.util.RandomNumberGeneratorUnix
-
Create an RNG using /dev/urandom as a source of random bits.
- RandomNumberGeneratorUnix(String) - Constructor for class etomica.util.RandomNumberGeneratorUnix
-
Create an RNG using the given file as a source of random bits.
- randomOrientation(IVectorMutable) - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- randomOrientation(IVectorMutable) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- randomPosition() - Method in interface etomica.box.RandomPositionSource
-
Returns a random position with the previously set box's boundary.
- randomPosition() - Method in class etomica.box.RandomPositionSourceDeformable
-
- randomPosition() - Method in class etomica.box.RandomPositionSourceRectangular
-
- randomPosition() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- RandomPositionSource - Interface in etomica.box
-
Interface for an object which returns random positions within a box's
boundary.
- RandomPositionSourceDeformable - Class in etomica.box
-
Implementation of RandomPositionSource that can handle
BoundaryDeformablePeriodic.
- RandomPositionSourceDeformable(ISpace, IRandom) - Constructor for class etomica.box.RandomPositionSourceDeformable
-
- RandomPositionSourceRectangular - Class in etomica.box
-
- RandomPositionSourceRectangular(ISpace, IRandom) - Constructor for class etomica.box.RandomPositionSourceRectangular
-
- randomRotation(IRandom, double) - Method in interface etomica.space.IOrientation
-
Perform a rotation by a random amount in the solid angle theta on the
present orientation.
- randomRotation(IRandom, double) - Method in class etomica.space2d.Orientation2D
-
Applies a random rotation of angle selected uniformly within plus or minus tStep
from the current value.
- randomRotation(IRandom, double) - Method in class etomica.space3d.Orientation3D
-
Applies a random rotation of angle selected uniformly from 0 to tStep.
- randomRotation(IRandom, double) - Method in class etomica.space3d.OrientationFull3D
-
Applies a random rotation of angle selected uniformly from 0 to tStep.
- randomSeeds - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- randomSeeds - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- randomSeeds - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- randomSeeds - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- range - Variable in class etomica.graphics.ColorSchemeTemperature
-
- range - Variable in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
- range - Variable in class etomica.modules.adsorption.MyMCMove
-
- range - Variable in class etomica.modules.adsorption.P1Wall
-
- range - Variable in class etomica.modules.colloid.P1Wall
-
- range - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- range - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- range - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- range - Variable in class etomica.nbr.cell.NeighborCellManager
-
- range - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- range - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- range - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- range - Variable in class etomica.nbr.list.PotentialMasterList
-
- range - Static variable in class org.jmol.script.Token
-
- RangeComparator() - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfined.RangeComparator
-
- rangedAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- rangedAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
-
- rangedAgentManager - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- rangedAgentManager - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- rangedPotentialIterator - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- rangedPotentialIterator - Variable in class etomica.nbr.PotentialMasterNbr
-
- RangePermutator - Class in etomica.graph.iterators
-
This is a facility class that iterates through (maxP1 - minP1 + 1) permutations one at
a time.
- RangePermutator(int, int, int) - Constructor for class etomica.graph.iterators.RangePermutator
-
- rangeselected - Static variable in class org.jmol.script.Token
-
- rasmol - Static variable in class org.jmol.script.Token
-
- RASTERIZER_SECURITY_POLICY - Static variable in class etomica.graph.view.rasterizer.Main
-
URL for Squiggle's security policy file
- RATIO - Static variable in class etomica.data.AccumulatorRatioAverage
-
- ratio - Variable in class etomica.data.AccumulatorRatioAverage
-
- RATIO - Static variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- ratio - Variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- RATIO - Static variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratio - Variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratio - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- RATIO - Static variable in class etomica.overlap.DataOverlap
-
- RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverage
-
- RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- RATIO_STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorRatioAverage
-
- ratioError - Variable in class etomica.data.AccumulatorRatioAverage
-
- ratioError - Variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- ratioError - Variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratioErrorStat - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- ratioMaxN - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- Rational - Class in etomica.util
-
Class handling rational numbers (numerator / denominator), including
addition, multiplication and reducing (15/6 => 5/2).
- Rational() - Constructor for class etomica.util.Rational
-
- Rational(int, int) - Constructor for class etomica.util.Rational
-
Creates Rational instance with the given numerator and denominator.
- Rational - Class in etomica.veos.bigdecimal
-
Fractions (rational numbers).
- Rational() - Constructor for class etomica.veos.bigdecimal.Rational
-
Default ctor, which represents the zero.
- Rational(BigInteger, BigInteger) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a numerator and denominator.
- Rational(BigInteger) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a numerator.
- Rational(int, int) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a numerator and denominator.
- Rational(int) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from an integer.
- Rational(String) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a string representation.
- Rational(String, int) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a string representation in a specified base.
- ratios - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- ratioStandardDeviation - Variable in class etomica.data.AccumulatorRatioAverage
-
- ratioStat - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- RAW_RGB - Static variable in class org.jmol.util.Colix
-
- rawData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- rawData2 - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- rawData3 - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- rawDataBlockSize - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- RawDataWindowOpener(int, DisplayPlot) - Constructor for class etomica.graphics.DisplayPlot.RawDataWindowOpener
-
- rBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- rBound(double, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
helper method that returns the position r if there are no bounds or
if r is inside the bounds or (if r is outside the bounds) returns the
position in the bounds nearest r.
- rc - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- rc - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- rc - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- rc - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- rc - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- rc - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- rc - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- rC - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- rC - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- rC - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- rC - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- rC - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- rC - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- rC - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- rC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- rc - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- rc - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- rc - Variable in class etomica.parser.ParserLAMMPS.Options
-
- rc0 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rc0 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rC1 - Variable in class etomica.meam.PotentialCuLREP
-
- rC1 - Variable in class etomica.meam.PotentialFeEAM
-
- rC1 - Variable in class etomica.meam.PotentialFeEAM_LS
-
- rC2 - Variable in class etomica.meam.PotentialCuLREP
-
- rC2 - Variable in class etomica.meam.PotentialFeEAM
-
- rC2 - Variable in class etomica.meam.PotentialFeEAM_LS
-
- rCc - Variable in class etomica.meam.PotentialEFS
-
- rCd - Variable in class etomica.meam.PotentialEFS
-
- RcData - Variable in class etomica.potential.P2QChemInterpolated
-
- rcLong - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- rcMax0 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rcMax0 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rcMax1 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rcMax1 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rcond - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- rcScale - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- rcScale - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- rcScale - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- rcShort - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- rcShort - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- rcShort - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- rCut - Variable in class etomica.models.water.P2Water4P
-
- rCut - Variable in class etomica.potential.EwaldSumMolecules
-
- rCut2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- rCut2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- rCut2 - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- rCutLJ - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- rCutLJ - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- rCutMax - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- rCutMax - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- rCutoff - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- rCutoff - Variable in class etomica.potential.P2MoleculeTruncated
-
- rCutoff - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- rCutoff - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- rCutoff - Variable in class etomica.potential.P2SoftTruncated
-
- rCutRealES - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- rCutRealES - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- rCutRealES - Variable in class etomica.potential.EwaldSummation
-
- rCutSquared - Variable in class etomica.potential.EwaldSummation
-
- rD - Variable in class etomica.data.meter.MeterPressureTensor
-
- rData - Variable in class etomica.data.meter.MeterRDF
-
- rData - Variable in class etomica.data.meter.MeterRDFPC
-
- rData - Variable in class etomica.potential.P2QChemInterpolated
-
- rdfdr - Variable in class etomica.virial.HypernettedChain
-
- rdfdr - Variable in class etomica.virial.PercusYevick
-
- rdfListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- rdfPump - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- rDistributionErrorHash - Variable in class etomica.virial.CalcFFT
-
- rDistributionHash - Variable in class etomica.virial.CalcFFT
-
- rdudr - Variable in class etomica.virial.PercusYevick1QC
-
- re - Static variable in class etomica.potential.P1HydrogenMielke
-
- ReactionEquilibrium - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibrium() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- ReactionEquilibriumGraphic - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibriumGraphic(ReactionEquilibrium, ISpace) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- ReactionEquilibriumGraphic.Applet - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibriumGraphic.MassEditor - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibriumGraphic.MySpeciesEditor - Class in etomica.modules.reactionequilibrium
-
- reactionField - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- reactionManagerCO - Variable in class etomica.modules.catalysis.Catalysis
-
- ReactionManagerCO - Class in etomica.modules.catalysis
-
- ReactionManagerCO(Catalysis) - Constructor for class etomica.modules.catalysis.ReactionManagerCO
-
- read(String) - Method in interface etomica.graph.engine.ConsoleReader
-
- read(String) - Method in class etomica.graph.engine.Interpreter
-
- read(Parser.CommandVariableValue) - Method in class etomica.graph.engine.Interpreter
-
- readData(String[]) - Method in class etomica.virial.MeterVirialBDBin
-
- readData(String[]) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- readData(String[]) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- readData(String[], int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readData(String[], int, boolean) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readDataReBin(String[], int, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readdb(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- readDistribution(int, boolean) - Method in class etomica.virial.CalcFFT
-
- ReaderIn - Class in etomica.eigenstuff
-
Reads in a file.
- ReaderIn() - Constructor for class etomica.eigenstuff.ReaderIn
-
- readFile(String, double[][]) - Static method in class etomica.util.numerical.AkimaSplineSmootherApp
-
- readFile(String, double[][]) - Static method in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- readFile(String, double[][]) - Static method in class etomica.util.numerical.AkimaSplineSmootherMain
-
- readLine(PipedInputStream) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- readMethod - Variable in class etomica.modifier.ModifierGeneral
-
- readOutputFile() - Method in class etomica.potential.PotentialEmul
-
- ReadParameters - Class in etomica.util
-
This class reads input parameters from a file and assigns the values to the
fields of an object.
- ReadParameters() - Constructor for class etomica.util.ReadParameters
-
- ReadParameters(String) - Constructor for class etomica.util.ReadParameters
-
- ReadParameters(String, ParameterBase) - Constructor for class etomica.util.ReadParameters
-
- readParameters() - Method in class etomica.util.ReadParameters
-
Reads each line from inputFileName and attempts to match it with a field
from parameterWrapper and sets the field to the value from the file.
- readProcessData(String, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readResolve() - Method in class etomica.graph.view.rasterizer.DestinationType
-
- readWeights(String) - Method in class etomica.virial.MeterVirialBDBin
-
- readWeights(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- readWeights(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- readWeights(String, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readWriteData(String[], String, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
This method reads all input files in parallel and writes lines out to
the new file as the bin data is known to be complete.
- ready - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- real() - Method in class etomica.math.Complex
-
Real part of this Complex number, the x-coordinate in rectangular coordinates.return Re[z] where z is this Complex number.
- REAL - Static variable in class etomica.util.Transform.Fourier
-
- realT - Variable in class etomica.normalmode.MeterHarmonicCoordinate
-
- realT - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- realT - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- realT - Variable in class etomica.normalmode.MeterNormalMode
-
- realYm(int, int, double, double) - Static method in class etomica.math.SphericalHarmonics
-
- reblockData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Reblock data from rawData2 into rawData3, then copy it back to rawData2
- reblockData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Reblock data from rawData into rawData2, taking blocks of size n
- rebuild(Object) - Method in interface etomica.util.DirtyObject
-
- Reciprocal() - Constructor for class etomica.util.Function.Reciprocal
-
- reclaim(IAtom) - Method in class etomica.association.ColorSchemeSmer
-
- recomputeColumnHeaders() - Method in class etomica.graphics.DisplayTable
-
Reconstruct the column headers array.
- recomputeCriteriaRanges() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Recomputes the range for all criterion based on our own range.
- recomputeCriteriaRanges() - Method in class etomica.nbr.list.PotentialMasterList
-
Recomputes the range for all criterion based on our own range.
- recomputeMoveFrequencies() - Method in class etomica.integrator.mcmove.MCMoveManager
-
Recomputes all the move frequencies.
- recomputeUnits() - Method in class etomica.graphics.DisplayTable
-
Reconstruct the units array.
- recomputeWeights() - Method in class etomica.virial.MeterVirialBDBin
-
- recomputeWeights() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long, boolean) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
- recomputeWeights() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long, boolean) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
- recomputeWeights() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, boolean, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
- reconfig - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- reconfig - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- Rectangle - Class in etomica.math.geometry
-
A 2-dimensional geometric rectangle.
- Rectangle(ISpace) - Constructor for class etomica.math.geometry.Rectangle
-
Constructs a square rectangle of unit size.
- Rectangle(ISpace, double, double) - Constructor for class etomica.math.geometry.Rectangle
-
Constructs a rectangle with edge lengths having the given values.
- RECTANGLE - Static variable in class g3dsys.control.G3DSys
-
- RectangleOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
-
- Rectangular - Interface in etomica.math.geometry
-
Interface for a polytope with shape that can be specified by the length
of D sides.
- RectangularLattice - Class in etomica.lattice
-
Basic implementation of the AbstractLattice interface, providing construction
and access of sites for a lattice of arbitrary dimension.
- RectangularLattice(int, SiteFactory) - Constructor for class etomica.lattice.RectangularLattice
-
Constructs a lattice of the given dimension (D) with sites
made from the given factory.
- RectangularLattice.Iterator - Class in etomica.lattice
-
Iterates over all sites of the lattice.
- RectangularLatticeNbrIterator - Class in etomica.lattice
-
An abstract iterator that generates the neighboring sites of a given site.
- RectangularLatticeNbrIterator(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIterator
-
Constructs iterator that needs to be configured before use.
- RectangularLatticeNbrIteratorAdjacent - Class in etomica.lattice
-
Iterates over the neighbors of a site, where neighbors are those
sites immediately adjacent to it in each direction; this does not
include sites diagonal to the site.
- RectangularLatticeNbrIteratorAdjacent(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIteratorAdjacent
-
- RectangularLatticeNbrIteratorSquare - Class in etomica.lattice
-
Iterates over neighbors of a site, where neighbors are defined as
those sites lying in a rectangular region centered on the site.
- RectangularLatticeNbrIteratorSquare(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
- recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- recursiveTag(IAtom) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- RED - Static variable in class org.jmol.util.Colix
-
- redColorScheme - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- redistributeForces(IMolecule, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Method in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- redomove - Static variable in class org.jmol.script.Token
-
- reduce(long, long) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- reduce(ArrayList<ClusterDiagram>) - Static method in class etomica.virial.cluster.ClusterOperations
-
Sorts cluster diagrams (but # of connections) and combines any diagrams
that are identical, resulting in a diagram with a weight equal to the
sum of the original weights.
- reducedTemp - Variable in class etomica.virial.CalcFFT
-
- ReeHoover - Class in etomica.graph.operations
-
This operation performs conversion from a set of biconnected graphs with f
edges to a set of diagrams of fully connected diagrams with e and f edges.
- ReeHoover() - Constructor for class etomica.graph.operations.ReeHoover
-
- ReeHoover.ReeHooverParameters - Class in etomica.graph.operations
-
- reeHooverCB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- ReeHooverMC - Class in etomica.virial.simulations
-
An implementation of MSMC with direct sampling for computation of
virial coefficients of hard spheres, in the spirit of Ree-Hoover Monte Carlo
(Ree & Hoover, 1964, Fifth and Sixth Virial Coefficients for Hard Spheres and
Hard Disks).
- ReeHooverMC() - Constructor for class etomica.virial.simulations.ReeHooverMC
-
- ReeHooverMC.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- ReeHooverParameters(char) - Constructor for class etomica.graph.operations.ReeHoover.ReeHooverParameters
-
- ReeHooverToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
-
- ref - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
-
- REF - Static variable in class etomica.overlap.DataOverlap
-
- ref - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- ref - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- ref - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- refAccumulator - Variable in class etomica.virial.overlap.DataSourceVirialOverlap
-
- refAccumulator - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- refAvg - Variable in class etomica.overlap.DataOverlap
-
- refAvg - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
-
- reference - Variable in class etomica.compatibility.FeatureRequirement
-
- referenceDataInterval - Variable in class etomica.normalmode.SimOverlapModule
-
- refErr - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
-
- refFrac - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- reflect() - Method in class etomica.normalmode.MeterSolidMirror
-
- refPref - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- refPref - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- refPref - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- refPref - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- refPref - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- refPref - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- refPref - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- refPref - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- refPref - Variable in class etomica.normalmode.MeterSamplingTarget
-
- refPref - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- refPref - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- refPref - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- refPref - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- refPref - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- refPref - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- refPref - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- refPref - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- refPref - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- refPref - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- refPref - Variable in class etomica.normalmode.SimBennet
-
- refPref - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- refPref - Variable in class etomica.normalmode.SimOverlap
-
- refPref - Variable in class etomica.normalmode.SimOverlapLJ
-
- refPref - Variable in class etomica.normalmode.SimOverlapLJModule
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- refPref - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- refPref - Variable in class etomica.normalmode.SimTargetUmbrella
-
- refPref - Variable in class etomica.normalmode.SimUmbrella
-
- refPref - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- refPref - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- refPref - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- refPref - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- refPrefFileName - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- refPrefFileName - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- refPrefFileName - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- refresh() - Method in class etomica.graphics.DevicePlotPoints
-
Instructs the plot to redisplay any plotted functions with the most
recent data.
- refresh() - Method in class g3dsys.control.G3DSys
-
For a thorough redraw of the display
- refreshAtomAgentMgr() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
refreshAtomAgentMgr() - sets the new atom manager based upon the box.
- refreshing - Static variable in class org.jmol.script.Token
-
- refreshSize() - Method in class etomica.graphics.DisplayBoxCanvas1D
-
- refreshSize() - Method in class etomica.graphics.DisplayBoxCanvas2D
-
- refreshSize() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- refSum - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- rejectNotify() - Method in class etomica.association.MCMoveBiasUB
-
- rejectNotify() - Method in class etomica.association.MCMoveBiasUBMolecule
-
- rejectNotify() - Method in class etomica.association.MCMoveDimer
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveDimerRotate
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveRotateAssociated
-
- rejectNotify() - Method in class etomica.association.MCMoveSmer
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveSmerRotate
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveVolumeAssociated
-
- rejectNotify() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- rejectNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMove
-
Method called by IntegratorMC in the event that the most recent trial
move is rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveAtom
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveDimer
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveRotate
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
Performs no action; nothing required when move rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- rejectNotify() - Method in class etomica.interfacial.MCMoveAtomNbr
-
- rejectNotify() - Method in class etomica.models.hexane.MCMoveCBMC
-
- rejectNotify() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- rejectNotify() - Method in class etomica.models.hexane.MCMoveReptate
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- rejectNotify() - Method in class etomica.modules.adsorption.MyMCMove
-
- rejectNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveHarmonic
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- rejectNotify() - Method in class etomica.normalmode.MCMovePhaseAngle
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveSingleMode
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveWV
-
- rejectNotify() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- rejectNotify() - Method in class etomica.spin.MCMoveSpinFlip
-
- rejectNotify() - Method in class etomica.virial.BoxCluster
-
Informs the box that the trial was rejected so it will go back to
the old coordinate pairs.
- rejectNotify() - Method in class etomica.virial.MCMoveChangeBondLength
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAngleBend
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtom
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSChain
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterDiagram
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterMolecule
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingScale
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- rejectNotify() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
- Relabel - Class in etomica.graph.operations
-
- Relabel() - Constructor for class etomica.graph.operations.Relabel
-
- relabel - Variable in class etomica.graph.property.FFTDecomposition
-
- relabel - Variable in class etomica.graph.property.IsFFT
-
- relabel(Graph) - Static method in class etomica.virial.IEGenerator
-
- RelabelParameters - Class in etomica.graph.operations
-
- RelabelParameters(byte[]) - Constructor for class etomica.graph.operations.RelabelParameters
-
- RelabelWertheim - Class in etomica.graph.operations
-
- RelabelWertheim() - Constructor for class etomica.graph.operations.RelabelWertheim
-
- relax() - Method in class etomica.space3d.OrientationFull3D
-
Normalizes both direction and secondaryDirection
- relaxAction - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- relaxInterval - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- relaxMolecule(IMolecule) - Method in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- releaseAgent(AtomArrayList, IAtom, IBox) - Method in class etomica.association.AssociationManager
-
- releaseAgent(Object, IMolecule) - Method in class etomica.association.AssociationManagerMolecule
-
- releaseAgent(ColorSchemeSmer.ColorAgent, IAtom, IBox) - Method in class etomica.association.ColorSchemeSmer
-
- releaseAgent(MCMoveVolumeAssociated.Agent, IAtom, IBox) - Method in class etomica.association.MCMoveVolumeAssociated
-
- releaseAgent(Object, IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- releaseAgent(E, IAtom, IBox) - Method in interface etomica.atom.AtomLeafAgentManager.AgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
- releaseAgent(Object, IAtomType) - Method in interface etomica.atom.AtomTypeAgentManager.AgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
- releaseAgent(Object, IAtomType) - Method in class etomica.atom.DiameterHashByType
-
- releaseAgent(Object, IMolecule) - Method in interface etomica.atom.MoleculeAgentManager.MoleculeAgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements
- releaseAgent(Object, ISpecies) - Method in interface etomica.atom.SpeciesAgentManager.AgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
- releaseAgent(E) - Method in interface etomica.box.BoxAgentManager.BoxAgentSource
-
- releaseAgent(AtomLeafAgentManager<E>) - Method in class etomica.box.BoxAgentSourceAtomManager
-
- releaseAgent(MoleculeAgentManager) - Method in class etomica.box.BoxAgentSourceMoleculeManager
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.dimer.IntegratorDimerMin
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.dimer.IntegratorDimerRT
-
- releaseAgent(Object, IAtom, IBox) - Method in class etomica.dimer.IntegratorEnergyMap
-
- releaseAgent(ArrayList, IAtom, IBox) - Method in class etomica.graphics.BondListener
-
- releaseAgent(Object, IAtomType) - Method in class etomica.graphics.ColorSchemeByType
-
- releaseAgent(Color, IAtom, IBox) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
-
- releaseAgent(Color, IAtom, IBox) - Method in class etomica.graphics.ColorSchemeRandom
-
- releaseAgent(Object, IMolecule) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
-
- releaseAgent(Ball[], IAtom, IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
-
- releaseAgent(Figure, IAtom, IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- releaseAgent(IntegratorConNVT.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorConNVT
-
- releaseAgent(IntegratorGear4.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorGear4
-
- releaseAgent(IntegratorHard.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorHard
-
- releaseAgent(Object, IAtomType) - Method in class etomica.integrator.IntegratorHard
-
- releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.integrator.IntegratorMD.VectorSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.integrator.IntegratorRigidIterative
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorRigidIterative
-
- releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorRigidIterative
-
- releaseAgent(IntegratorRigidMatrixIterative.AtomAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- releaseAgent(Object, IMolecule) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- releaseAgent(IntegratorVerlet.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorVerlet
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedU
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedVirial
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedVirialV
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMeanForce
-
- releaseAgent(EwaldSummation.MyCharge, IAtom, IBox) - Method in class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
-
- releaseAgent(Object, IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
-
- releaseAgent(EwaldSummation.MyCharge, IAtom, IBox) - Method in class etomica.models.water.ChargeAgentSourceTIP4PWater
-
- releaseAgent(InteractionTracker.CatalysisAgent, IAtom, IBox) - Method in class etomica.modules.catalysis.InteractionTracker
-
- releaseAgent(AtomFilterChainLength.LengthAgent, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- releaseAgent(IAtom[], IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- releaseAgent(ColorSchemeRadical.LengthAgent, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- releaseAgent(Object, IAtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- releaseAgent(IAtom[], IAtom, IBox) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- releaseAgent(MeterChainLength.AtomTag, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- releaseAgent(Boolean, IAtom, IBox) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- releaseAgent(IntegratorDroplet.MyAgent, IAtom, IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- releaseAgent(IAtom, IAtom, IBox) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- releaseAgent(Object, IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
-
- releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.modules.rosmosis.P1Tether
-
- releaseAgent(Object, IMolecule) - Method in class etomica.modules.sam.CriterionTether3
-
- releaseAgent(NeighborCellManager) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- releaseAgent(NeighborCellManagerMolecular) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Removes the given atom from the cell.
- releaseAgent(Cell, IAtom, IBox) - Method in class etomica.nbr.cell.NeighborCellManager
-
Removes the given atom from the cell.
- releaseAgent(CriterionPositionWall.DoubleWrapper, IAtom, IBox) - Method in class etomica.nbr.CriterionPositionWall
-
- releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.nbr.CriterionSimple
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- releaseAgent(NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- releaseAgent(AtomPotentialList, IAtom, IBox) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- releaseAgent(AtomNeighborLists, IAtom, IBox) - Method in class etomica.nbr.list.NeighborListManager
-
- releaseAgent(NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- releaseAgent(Object, ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- releaseAgent(Object, IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
-
- releaseAgent(Object, ISpecies) - Method in class etomica.nbr.PotentialMasterNbr
-
- releaseAgent(AtomSite, IAtom, IBox) - Method in class etomica.nbr.site.NeighborSiteManager
-
- releaseAgent(BoxCellManager) - Method in class etomica.nbr.site.PotentialMasterSite.BoxAgentSiteSource
-
- releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.normalmode.CoordinateDefinition.SiteSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
-
- releaseAgent(HSNPT.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.MeterDADB
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.MeterSolidProps
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.MeterSolidPropsLJ
-
- releaseAgent(Object, IAtom, IBox) - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
-
- releaseAgent(Object, IMolecule) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
-
- releaseAgent(P2HardBondedList.BondArrayList, IAtom, IBox) - Method in class etomica.potential.P2HardBondedList
-
- releaseAgent(AtomArrayList, IAtom, IBox) - Method in class etomica.potential.P2SquareWellRobust
-
- releaseAgent(Object, IAtomType) - Method in class etomica.potential.PotentialMasterMonatomic
-
- releaseAgent(IntegratorVelocityVerletQuaternion.AtomAgent, IAtom, IBox) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- releaseAgent(Object, IMolecule) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- releaseAgent(Object, ISpecies) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- releaseAgent(Integrator.Forcible, IAtom, IBox) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- releaseAgent(NeighborCellManagerThreaded) - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.util.numerical.CalcGradientDifferentiable
-
- releaseBond(Object) - Method in interface etomica.graphics.BondManager
-
Notifies the BondManager that the given bond no longer exists in the
system.
- releaseBond(Object) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Removes the given bond from the graphical display.
- releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
-
- releaseScreenImage() - Method in class org.jmol.util.GData
-
- remove(int) - Method in class etomica.atom.AtomArrayList
-
This removes the atom at the given index and shifts the remaining atoms
back (maintaining the order).
- remove(int) - Method in class etomica.atom.MoleculeArrayList
-
- remove() - Method in class etomica.graph.iterators.CartesianIterator
-
- remove() - Method in class etomica.graph.iterators.CartesianPermutator
-
- remove() - Method in class etomica.graph.iterators.ChainedIterator
-
- remove() - Method in class etomica.graph.iterators.DefaultIterator
-
- remove() - Method in class etomica.graph.iterators.DefaultPermutator
-
- remove() - Method in class etomica.graph.iterators.EdgelessIterator
-
- remove() - Method in class etomica.graph.iterators.filters.GlobalFilter
-
- remove() - Method in class etomica.graph.iterators.filters.LocalFilter
-
- remove() - Method in class etomica.graph.iterators.FixedEdgeCountIterator
-
- remove() - Method in class etomica.graph.iterators.IteratorWrapper
-
- remove() - Method in class etomica.graph.iterators.RangePermutator
-
- remove() - Method in class etomica.graph.iterators.StoredIterator
-
- remove(Object) - Method in class etomica.graph.model.GraphList
-
- remove(Display) - Method in class etomica.graphics.SimulationGraphic
-
- remove(Device) - Method in class etomica.graphics.SimulationGraphic
-
- remove(int) - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- remove(IFunction) - Method in class etomica.util.FunctionChain
-
Removes the given function from the chain.
- remove(int) - Method in class etomica.util.ObjectArrayList
-
Removes the element at the specified position in this list.
- remove() - Method in class etomica.util.TreeLinker
-
Disconnects this linker from the linkers above and below it, and
puts them in sequence, repairing the hole.
- remove(TreeLinker) - Static method in class etomica.util.TreeList
-
- remove() - Method in class etomica.virial.PYGenerator.IteratorEF
-
- removeAction(IAction) - Method in interface etomica.action.ActionGroup
-
Removes the given oldAction from the group.
- removeAction(IAction) - Method in class etomica.action.ActionGroupSeries
-
Removes the given action from the group.
- removeAction(IAction) - Method in class etomica.action.activity.ActivityGroupParallel
-
- removeAction(IAction) - Method in class etomica.action.activity.ActivityGroupSeries
-
Removes the given action from the list of actions performed by this controller.
- removeAction(IAction) - Method in class etomica.action.activity.Controller
-
- removeAll(Collection<?>) - Method in class etomica.graph.model.GraphList
-
- removeAllValueChangedListeners() - Method in class etomica.graphics.DeviceBox
-
Removes all objects that are listening for a value changed event.
- removeAndReplace(int) - Method in class etomica.atom.AtomArrayList
-
This removes the atom at the given index and replaces the hole with the
last atom.
- removeAndReplace(int) - Method in class etomica.atom.MoleculeArrayList
-
- removeAtom(IAtom) - Method in class etomica.nbr.cell.Cell
-
- removeAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerLJadatom
-
- removeAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMadatom
-
- removeAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMGB
-
- removeAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCLJadatom
-
- removeAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCMEAMadatom
-
- removeBox(IBox) - Method in interface etomica.api.ISimulation
-
Removes a Box to the simulation.
- removeBox(IBox) - Method in class etomica.simulation.Simulation
-
- removeChildAtom(IAtom) - Method in class etomica.atom.Molecule
-
Removes the given child Atom from this AtomGroup.
- removeChildType(IAtomType) - Method in class etomica.species.Species
-
- removeChildType(IAtomType) - Method in class etomica.species.SpeciesSpheresHetero
-
Removes the given factory as a child of this factory.
- removeCollisionListener(IntegratorHard.CollisionListener) - Method in class etomica.integrator.IntegratorHard
-
De-registers an object from the list of collision listeners.
- removeCountOfSpeciesSLMListener(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- removeData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- removeData() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- removeDataListener(DataSetListener) - Method in class etomica.data.DataSet
-
- removeDataSink(IDataSink) - Method in class etomica.data.DataFork
-
- removeDataSink(IDataSink) - Method in interface etomica.data.DataPipeForked
-
Removes the specified data sink.
- removeDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
-
Removes the specified data sink.
- removeDrawable(Drawable) - Method in class etomica.graphics.DisplayBox
-
- removeDrawable(Object) - Method in class etomica.graphics.DisplayBox
-
- removeFig(Figure) - Method in class g3dsys.control.G3DSys
-
Removes the Figure to from associated FigureManager
- removeIntegrator(IIntegrator) - Method in class etomica.integrator.IntegratorManagerMC
-
Removes the given integrator from the list of integrators.
- removeLine(LineSegment) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- removeListener(IBoundaryListener) - Method in interface etomica.api.IBoundaryEventManager
-
Removes the given listener from this event manager.
- removeListener(IBoxListener) - Method in interface etomica.api.IBoxEventManager
-
Removes the given listener from this event manager.
- removeListener(IIntegratorListener) - Method in interface etomica.api.IIntegratorEventManager
-
Removes the given listener from this event manager.
- removeListener(ISimulationListener) - Method in interface etomica.api.ISimulationEventManager
-
- removeListener(IBoxListener) - Method in class etomica.box.BoxEventManager
-
- removeListener(DeviceTernarySelector.Listener) - Method in class etomica.graphics.DeviceTernarySelector
-
- removeListener(IIntegratorListener) - Method in class etomica.integrator.IntegratorEventManager
-
- removeListener(IIntegratorListener) - Method in class etomica.listener.IntegratorListenerGroupSeries
-
Removes the given action from the group.
- removeListener(IListener) - Method in interface etomica.listener.ListenerGroup
-
Removes the given oldAction from the group.
- removeListener(INeighborListListenerMolecular) - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
-
- removeListener(INeighborListListener) - Method in class etomica.nbr.list.NeighborListEventManager
-
- removeListener(ISimulationListener) - Method in class etomica.simulation.SimulationEventManager
-
- removeListener(IBoundaryListener) - Method in class etomica.space.BoundaryEventManager
-
- removeListener(IListener) - Method in class etomica.util.EventManager
-
- removeListener(IListener) - Method in interface etomica.util.IEventManager
-
Removes the given listener from this event manager.
- removeMCMove(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Removes the given MCMove from the set of moves performed by the integrator and
recalculates move frequencies.
- removeModel(Model) - Method in class etomica.graphics.BondListener
-
Informs the BondListener that bonds in molecules of the given model
should no longer be tracked.
- removeMolecule(IMolecule) - Method in interface etomica.api.IBox
-
Removes the given molecule from this box.
- removeMolecule(IMolecule) - Method in class etomica.box.Box
-
- removeMolecule(IMolecule) - Method in class etomica.nbr.cell.molecule.CellMolecular
-
- removeMoleculeListDisplayLSMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removeMoleculeListDisplayLSMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removeMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeObject(Object[], Object) - Static method in class etomica.util.Arrays
-
Returns an array formed by removing the given object from the given array.
- removeObjectByBox(IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- removeOption(String) - Method in class etomica.graphics.DeviceSelector
-
- removeParser(ParameterParser) - Method in class etomica.util.ParameterBase
-
- removePlane(Plane) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- removePotential(IPotentialMolecular) - Method in interface etomica.api.IPotentialMaster
-
Removes given potential from the group.
- removePotential(IPotentialAtomic) - Method in interface etomica.api.IPotentialMaster
-
Removes given potential from the group.
- removePotential(IPotentialMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.list.PotentialMasterList
-
- removePotential(IPotentialMolecular) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialGroupNbr
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialMasterHybrid
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialMasterNbr
-
- removePotential(IPotential) - Method in class etomica.potential.PotentialArray
-
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
- removePotential(IPotential) - Method in class etomica.potential.PotentialArrayByType
-
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
- removePotential(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular
-
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
- removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup
-
Removes given potential from the group.
- removePotential(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
-
- removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMaster
-
- removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMasterMonatomic
-
- removePotentialJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removePotentialJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removePotParamDisplayLSMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removePotParamDisplayLSMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removePotParamDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removePotParamDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- removeRange(int, int) - Method in class etomica.util.ObjectArrayList
-
Removes from this List all of the elements whose index is between
fromIndex, inclusive and toIndex, exclusive.
- removeSpecies(ISpecies) - Method in interface etomica.api.ISimulation
-
Removes the given ISpecies from the ISimulation.
- removeSpecies(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
- removeSpecies(ISpecies) - Method in class etomica.simulation.Simulation
-
- removeSpecies() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- removeSpeciesAtIndex(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- removeSpeciesJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removeSpeciesJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeSpeciesMolecule(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- removeSpeciesNotify(ISpecies) - Method in interface etomica.api.IBox
-
Notifies the IBox that a Species has been removed.
- removeSpeciesNotify(ISpecies) - Method in class etomica.box.Box
-
- removeValueChangedListener(DeviceBoxValueChangedListener) - Method in class etomica.graphics.DeviceBox
-
Remove an object that is listening for the DeviceBox value to change
- renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
-
- renderAllStrings(Object) - Method in class org.jmol.util.GData
-
- renderBackground(Graphics3D) - Method in class org.jmol.g3d.Graphics3D
-
- renderBackground(Graphics3D) - Method in class org.jmol.util.GData
-
- renderCrossHairs(int[], int, int, Point3f, float) - Method in class org.jmol.g3d.Graphics3D
-
- renderHermiteRibbon(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, int) - Method in class org.jmol.g3d.HermiteRenderer
-
- renderHermiteRope(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.HermiteRenderer
-
- RenderMD - Class in etomica.modules.render
-
Three-dimensional hard-sphere molecular dynamics simulation, using
neighbor listing.
- RenderMD(ISpace) - Constructor for class etomica.modules.render.RenderMD
-
Sole public constructor, makes a simulation using a 3D space.
- RenderMD(ISpace, RenderMD.RenderMDParam) - Constructor for class etomica.modules.render.RenderMD
-
- RenderMD.CriterionCar - Class in etomica.modules.render
-
- RenderMD.P2PenetrableCar - Class in etomica.modules.render
-
- RenderMD.RenderMDParam - Class in etomica.modules.render
-
Inner class for parameters understood by the HSMD3D constructor
- RenderMDGraphic - Class in etomica.modules.render
-
- RenderMDGraphic(RenderMD, Space) - Constructor for class etomica.modules.render.RenderMDGraphic
-
- RenderMDParam() - Constructor for class etomica.modules.render.RenderMD.RenderMDParam
-
- repaint() - Method in class etomica.graphics.Display
-
- repaint() - Method in class etomica.graphics.DisplayBox
-
Repaint the graphic associated with the display box.
- repaint() - Method in class etomica.graphics.DisplayCanvas
-
- repaint() - Method in class etomica.graphics.DisplayPolytope
-
- repaint() - Method in class etomica.graphics.DisplayTable
-
- repaint() - Method in class etomica.graphics.PropertyText
-
- repaint(Object) - Method in interface org.jmol.api.ApiPlatform
-
- repaint(Object) - Method in class org.jmol.awt.Platform
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
-
- repaintSleep - Variable in class etomica.graphics.SimulationGraphic
-
- repaintwaitms - Static variable in class org.jmol.script.Token
-
- replaceAllCharacter(String, String, char) - Static method in class org.jmol.util.TextFormat
-
Does a clean replace of any of the characters in str with chrTo
If strTo contains strFrom, then only a single pass is done.
- replaceAllCharacters(String, String, String) - Static method in class org.jmol.util.TextFormat
-
Does a clean replace of any of the characters in str with strTo
If strTo contains strFrom, then only a single pass is done.
- replaceQuotedStrings(Vector, Vector, String, int) - Static method in class etomica.util.ScientificFormat
-
- replaceQuotedStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
-
- replaceStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
-
- replicate(Configuration, IBox, int[], ISpace) - Static method in class etomica.config.ConfigurationFileBinary
-
Reads the configuration from the file and then replicates the
configuration reps times in each direction.
- replicate(Configuration, IBox, int[], ISpace) - Static method in class etomica.config.ConfigurationReplicate
-
Replicates the configuration from config within boxBig.
- REPULSION_ATTRACTION - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- REPULSION_ONLY - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- requestFocusInWindow(Object) - Method in interface org.jmol.api.ApiPlatform
-
- requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
-
- Requirement - Class in etomica.compatibility
-
- Requirement() - Constructor for class etomica.compatibility.Requirement
-
- RequirementSet - Class in etomica.compatibility
-
- rescale(Configuration, IBox, double, ISpace) - Static method in class etomica.config.ConfigurationFileBinary
-
- rescaleBox(double) - Method in class etomica.normalmode.SimFluidSoftSphere
-
- rescalingToFitVolume - Variable in class etomica.config.ConfigurationLattice
-
- rescalingToFitVolume - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- rescalingToFitVolume - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- reservoir - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- reservoirCount - Variable in class etomica.box.Box
-
- reservoirSize - Variable in class etomica.atom.AtomLeafAgentManager
-
- reservoirSize - Variable in class etomica.atom.MoleculeAgentManager
-
- reservoirSize - Variable in class etomica.box.Box
-
- reset() - Method in class etomica.action.activity.ActivityGroupSeries
-
Marks all actions as pending.
- reset() - Method in class etomica.action.activity.Controller
-
- RESET - Static variable in class etomica.action.activity.ControllerEvent
-
- reset() - Method in interface etomica.action.activity.IController
-
Marks all actions as pending.
- reset() - Method in interface etomica.api.IIntegrator
-
Defines the actions taken by the integrator to reset itself, such as
required if a perturbation is applied to the simulated box (e.g.,
addition or deletion of a molecule).
- reset() - Method in class etomica.atom.AtomLeafAgentManager.AgentIterator
-
- reset() - Method in class etomica.atom.AtomTypeAgentManager.AgentIterator
-
- reset() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- reset() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- reset() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- reset() - Method in class etomica.atom.iterator.ApiIndexList
-
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
- reset() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Resets the iterator, so that it is ready to go through all of its pairs.
- reset() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.ApiIntergroup
-
- reset() - Method in class etomica.atom.iterator.ApiIntergroupCoupled
-
- reset() - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
- reset() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.ApiIntragroup
-
Puts iterator in a state to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
- reset() - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Readies the iterator to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Puts iterator in a state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Puts iterator in a state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- reset() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
Resets iterator to a state where hasNext is true.
- reset() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
- reset() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
- reset() - Method in interface etomica.atom.iterator.AtomsetIterator
-
Resets the iterator to loop through its iterates again.
- reset() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- reset() - Method in class etomica.atom.iterator.MoleculeIteratorAll
-
- reset() - Method in class etomica.atom.iterator.MoleculeIteratorArrayList
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.MoleculeIteratorMolecule
-
- reset() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet
-
Resets iterator to a state where hasNext is true.
- reset() - Method in class etomica.atom.iterator.MpiInnerFixed
-
Resets the iterator, so that it is ready to go through all of its pairs.
- reset() - Method in class etomica.atom.iterator.MpiInnerVariable
-
Resets the iterator, so that it is ready to go through all of its pairs.
- reset() - Method in class etomica.atom.iterator.MpiInterArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.MpiInterspecies1A
-
- reset() - Method in class etomica.atom.iterator.MpiInterspeciesAA
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.MpiIntraArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.MpiIntraspecies1A
-
- reset() - Method in class etomica.atom.iterator.MpiIntraspeciesAA
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.MpiMolecule
-
Readies iterator for iteration.
- reset() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- reset() - Method in class etomica.atom.MoleculeAgentManager.AgentIterator
-
- reset() - Method in class etomica.atom.SpeciesAgentManager.AgentIterator
-
- reset() - Method in class etomica.box.BoxAgentManager.AgentIterator
-
- reset() - Method in class etomica.config.ConformationChain
-
Resets the vector instructions.
- reset() - Method in class etomica.config.ConformationChain2D
-
- reset() - Method in class etomica.config.ConformationChain3D
-
- reset() - Method in class etomica.config.ConformationChainZigZag
-
- reset() - Method in class etomica.config.ConformationChainZigZag2
-
- reset() - Method in class etomica.data.AccumulatorAverage
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageBlockless
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCollapsing
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCovariance
-
- reset() - Method in class etomica.data.AccumulatorAverageFixed
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorCounter
-
Sets count to zero.
- reset() - Method in class etomica.data.AccumulatorHistogram
-
Zeros histograms, discarding any previous contributions.
- reset() - Method in class etomica.data.AccumulatorHistory
-
- reset() - Method in class etomica.data.AccumulatorRatioAverage
-
- reset() - Method in class etomica.data.AccumulatorRatioAverageCovariance
-
- reset() - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- reset() - Method in class etomica.data.DataAccumulator
-
Defined by subclass to perform some action that clears accumulated values.
- reset() - Method in class etomica.data.DataArrayWriter
-
- reset() - Method in interface etomica.data.DataLogger.DataWriter
-
Informs the DataSink that it will be writing the beginning of the
file so printing header information is appropriate.
- reset() - Method in class etomica.data.DataPumpListenerPow
-
- reset() - Method in class etomica.data.DataPumpListenerPowStrict
-
- reset() - Method in class etomica.data.DataSet
-
- reset() - Method in class etomica.data.DataTableWriter
-
- reset() - Method in class etomica.data.meter.MeterDihedralAngle
-
Zero's out the G(phi) sum tracked by this meter.
- reset() - Method in class etomica.data.meter.MeterMeanSquareDisplacement
-
Specifies the set of atoms that will be tracked to compute their MSD.
- reset() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- reset() - Method in class etomica.data.meter.MeterPressureHard
-
- reset() - Method in class etomica.data.meter.MeterProfile
-
- reset() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- reset() - Method in class etomica.data.meter.MeterProfileByVolume
-
- reset() - Method in class etomica.data.meter.MeterRDF
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.data.meter.MeterRDFPC
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.data.meter.MeterStructureFactor
-
- reset() - Method in class etomica.data.meter.PotentialCalculationRDF
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.dimer.IntegratorDimerMin
-
- reset() - Method in class etomica.dimer.IntegratorDimerRT
-
- reset() - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
Zeros out the pressureTensor.
- reset() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- reset() - Method in class etomica.graphics.DeviceControllerButton
-
Sets label of button to display "Start".
- reset() - Method in class etomica.graphics.DeviceTrioControllerButton
-
Sets controller toggle button to read "Start"
- reset() - Method in class etomica.integrator.Integrator
-
Defines the actions taken by the integrator to reset itself, such as
required if a perturbation is applied to the simulated box (e.g.,
addition or deletion of a molecule).
- reset() - Method in class etomica.integrator.IntegratorBox
-
Defines the actions taken by the integrator to reset itself, such as
required if a perturbation is applied to the simulated box (e.g.,
addition or deletion of a molecule).
- reset() - Method in class etomica.integrator.IntegratorGear4
-
- reset() - Method in class etomica.integrator.IntegratorGear4NPH
-
- reset() - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
resets the "atom" held by this class, ensuring the method will
work even if (coincidentally) the atom is the same as the same
one as the last time the method was called.
- reset() - Method in class etomica.integrator.IntegratorHard
-
- reset() - Method in class etomica.integrator.IntegratorManagerMC
-
Causes recalculation of move frequencies and zero of selection counts for
moves.
- reset() - Method in class etomica.integrator.IntegratorMC
-
Causes recalculation of move frequencies and zero of selection counts for
moves.
- reset() - Method in class etomica.integrator.IntegratorMD
-
reset the integrator's kinetic energy tracker
- RESET - Static variable in class etomica.integrator.IntegratorNonintervalEvent
-
- reset() - Method in class etomica.integrator.IntegratorRigidIterative
-
- reset() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- reset() - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- reset() - Method in class etomica.integrator.IntegratorVelocityVerletRattle
-
- reset() - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- reset() - Method in class etomica.integrator.IntegratorVerlet
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveTracker
-
- reset() - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
Re-zeros the force vector.
- reset() - Method in class etomica.lattice.CellLattice.NeighborIterator
-
- reset() - Method in interface etomica.lattice.IndexIterator
-
- reset() - Method in class etomica.lattice.IndexIteratorIncreasing
-
Resets the iterator.
- reset() - Method in class etomica.lattice.IndexIteratorRectangular
-
Puts iterator in a condition to begin iteration.
- reset() - Method in class etomica.lattice.IndexIteratorReflecting
-
- reset() - Method in class etomica.lattice.IndexIteratorTriangular
-
Sets iterator to begin returning iterates.
- reset() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
-
- reset() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- reset() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Resets the iterator to loop through its iterates again.
- reset() - Method in interface etomica.lattice.SiteIterator
-
Puts the iterator in a state ready to begin iteration.
- reset() - Method in class etomica.mappedvirial.MappedUpotential
-
- reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- reset() - Method in class etomica.math.discrete.CombinationIterator
-
- reset() - Method in class etomica.math.discrete.FixedSumIterator
-
Sets the iterator to begin iteration.
- reset() - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Readies the iterator for iteration.
- reset() - Method in class etomica.math.discrete.PermutationIterator
-
- reset() - Method in class etomica.metastable.MeterDensityDistribution
-
- reset() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.modules.adsorption.EOSSW
-
- reset() - Method in class etomica.modules.adsorption.EOSSWPatel
-
- reset() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- reset() - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- reset() - Method in class etomica.modules.adsorption.ModifierPMu
-
- reset() - Method in class etomica.modules.adsorption.VEOS3SW
-
- reset() - Method in class etomica.modules.catalysis.InteractionTracker
-
- reset() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- reset(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- reset() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- reset() - Method in class etomica.modules.droplet.IntegratorDroplet
-
- reset() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- reset() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- reset() - Method in class etomica.modules.joulethomson.IntegratorJT
-
- reset() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
-
- reset() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- reset() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Resets all sums to zero
- reset() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- reset() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- reset() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- reset(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- reset() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
Re-zeros the force vectors.
- reset() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
Re-zeros the force vectors.
- reset(IAtom) - Method in class etomica.modules.sam.CriterionTether3
-
- reset() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- reset() - Method in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- reset() - Method in class etomica.nbr.cell.Api1ACell
-
- reset() - Method in class etomica.nbr.cell.ApiAACell
-
- reset() - Method in class etomica.nbr.cell.AtomIteratorCell
-
- reset() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- reset() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- reset() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- reset() - Method in class etomica.nbr.cell.PotentialMasterCell
-
Reassign atoms to cell lists for all boxes.
- reset(IAtom) - Method in class etomica.nbr.CriterionAdapter
-
Indicates to wrapped criterion that given atom's neighbor list has just
been updated, and that properties (e.g., record of atom's position) used
by needUpdate and unsafe() methods should be reset.
- reset(IAtom) - Method in class etomica.nbr.CriterionAll
-
Performs no action.
- reset(IAtom) - Method in class etomica.nbr.CriterionNone
-
Performs no action.
- reset(IAtom) - Method in class etomica.nbr.CriterionPositionWall
-
- reset(IAtom) - Method in class etomica.nbr.CriterionSimple
-
- reset() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
For each box in the array, applies central image,
resets neighbors of all atoms, and sets up all neighbor
lists.
- reset() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Recomputes the maximum potential range (which might change without this
class receiving notification) and readjust cell lists
- reset() - Method in class etomica.nbr.list.NeighborListManager
-
For each box in the array, applies central image,
resets neighbors of all atoms, and sets up all neighbor
lists.
- reset() - Method in class etomica.nbr.list.PotentialMasterList
-
Recomputes the maximum potential range (which might change without this
class receiving notification) and readjust cell lists
- reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Indicates to wrapped criterion that given atom's neighbor list has just
been updated, and that properties (e.g., record of atom's position) used
by needUpdate and unsafe() methods should be reset.
- reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Performs no action.
- reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- reset(IMolecule) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
Indicates to criterion that given molecule's neighbor list has just been
updated, and that properties (e.g., record of molecule's position)
used by needUpdate and unsafe() methods should be reset.
- reset(IAtom) - Method in interface etomica.nbr.NeighborCriterion
-
Indicates to criterion that given atom's neighbor list has just been
updated, and that properties (e.g., record of atom's position)
used by needUpdate and unsafe() methods should be reset.
- reset() - Method in class etomica.nbr.site.Api1ASite
-
- reset() - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- reset() - Method in class etomica.normalmode.IntegratorHardMDMC
-
- reset() - Method in class etomica.normalmode.MeterNormalMode
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.normalmode.MeterTiltHistogram
-
- reset() - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- reset() - Method in class etomica.normalmode.PotentialCalculationEFSSP
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- reset() - Method in class etomica.normalmode.PotentialCalculationLJSP
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- reset() - Method in class etomica.overlap.IntegratorOverlap
-
- reset() - Method in class etomica.potential.PotentialCalculationForcePressureSum
-
Zeros out the pressureTensor.
- reset() - Method in class etomica.potential.PotentialCalculationForceSum
-
Re-zeros the force vectors.
- reset() - Method in class etomica.potential.PotentialCalculationTorqueSum
-
Re-zeros the force vectors.
- reset() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- reset() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- reset() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- reset() - Method in interface etomica.space.RotationTensor
-
Sets tensor to a condition of no rotation.
- reset() - Method in class etomica.space2d.RotationTensor2D
-
- reset() - Method in class etomica.space3d.RotationTensor3D
-
- reset() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Resets this integrator and passes on the reset to the subIntegrator.
- reset() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- reset() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- reset() - Method in interface etomica.util.Histogram
-
resets all histogram values and counts to zero
- reset() - Method in class etomica.util.HistogramCollapsing
-
- reset() - Method in class etomica.util.HistogramDiscrete
-
- reset() - Method in class etomica.util.HistogramExpanding
-
- reset() - Method in class etomica.util.HistogramNotSoSimple
-
- reset() - Method in class etomica.util.HistogramReweightedData
-
- reset() - Method in class etomica.util.HistogramSimple
-
- reset() - Method in interface etomica.util.History
-
Resets the History.
- reset() - Method in class etomica.util.HistoryCollapsing
-
Removes entire history, setting all values to NaN.
- reset() - Method in class etomica.util.HistoryCollapsingAverage
-
- reset() - Method in class etomica.util.HistoryComplete
-
Removes entire history, setting all values to NaN.
- reset() - Method in class etomica.util.HistoryScrolling
-
Removes entire history, setting all values to NaN.
- reset() - Method in class etomica.util.TreeList
-
clear the tree by disconnecting everything from the head.
- reset() - Method in class etomica.virial.cluster.ClusterDiagram
-
Resets the cluster to being fully connected except that root points
are not connected to each other.
- reset() - Method in class etomica.virial.cluster.ClusterGenerator
-
Resets the cluster generator.
- reset() - Method in class etomica.virial.cluster.PermutationIterator
-
- reset(long) - Method in class etomica.virial.CoordinatePairLeafSet
-
- reset(long) - Method in class etomica.virial.CoordinatePairMoleculeSet
-
- reset(long) - Method in interface etomica.virial.CoordinatePairSet
-
Informs the CoordinatePairSet that the configuration has changed and that it
has a new ID
- reset() - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
-
- reset() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
Reset to initial value.
- reset() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- reset() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- reset() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- reset() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- reset() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- reset() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Resets all sums to zero
- reset() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Convenience method that resets reference and target accumulators
- reset() - Method in class etomica.virial.overlap.DataVirialOverlap
-
Convenience method that resets reference and target accumulators
- reset() - Method in class etomica.virial.overlap.IntegratorOverlap
-
- reset() - Method in interface g3dsys.control.IndexIterator
-
Resets iteration; should be called before use
- reset() - Method in class org.jmol.util.BoxInfo
-
- ResetAccumulators - Class in etomica.action
-
- ResetAccumulators() - Constructor for class etomica.action.ResetAccumulators
-
- ResetAccumulatorsAveraged - Class in etomica.action
-
- ResetAccumulatorsAveraged() - Constructor for class etomica.action.ResetAccumulatorsAveraged
-
- resetAction - Variable in class etomica.graphics.DeviceNSelector
-
- resetAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- resetAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- resetAdjustStep() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Resets damped step adjustment.
- resetAxes() - Method in class etomica.graphics.EtomicaPlot
-
Overrides a not-so-useful method in superclass
- resetBonds() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- resetBonds() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- resetCollision() - Method in class etomica.integrator.IntegratorHard.Agent
-
resets collision potential and partner.
- resetCollisionFull() - Method in class etomica.integrator.IntegratorHard.Agent
-
resets time, potential and partner.
- resetCollisionTimes() - Method in class etomica.integrator.IntegratorHard
-
Do an upList call for each atom and reconstruct the event list.
- resetFilter() - Method in interface etomica.atom.AtomFilterCollective
-
Informs the filter that something in the system has changed (atom
positions, velocityies, etc) has changed and the filtered status of the
atoms should be determined.
- resetFilter() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquid
-
- resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- resetNewMoleculePair() - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- resetNewMoleculePair() - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- resetPiston() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- resetRotation() - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- resetScale() - Method in class etomica.graphics.DisplayScrollingGraph
-
- resetSelectionViewANew() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- resetSlab() - Method in class org.jmol.util.MeshSurface
-
- resetStepCount() - Method in interface etomica.api.IIntegrator
-
This method resets the step counter.
- resetStepCount() - Method in class etomica.integrator.Integrator
-
- resetStepCount() - Method in class etomica.integrator.IntegratorMD
-
- resetStepCount() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- resetViewAfterSSSPException() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- resetViewToDisplaySpecies1() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- reshape(int, int) - Method in class etomica.graphics.DisplayCanvas
-
Same as setSize, but included to implement DisplayCanvasInterface,
which has this for compatibility with OpenGL.
- residual - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- residue - Static variable in class org.jmol.script.Token
-
- resizeArray(Object[], int) - Static method in class etomica.util.Arrays
-
Returns a new array holding the objects in the given array, but adjusted
to the given size.
- resizeArray(double[], int) - Static method in class etomica.util.Arrays
-
Returns a new array holding the values in the given array, but adjusted
to the given size.
- resizeArray(int[], int) - Static method in class etomica.util.Arrays
-
Returns a new array holding the values in the given array, but adjusted
to the given size.
- resizeArray(long[], int) - Static method in class etomica.util.Arrays
-
- resizeArray(boolean[], int) - Static method in class etomica.util.Arrays
-
Returns a new array holding the values in the given array, but adjusted
to the given size.
- resizeData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- resizeData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
- resizeDimer() - Method in class etomica.dimer.IntegratorDimerRT
-
- resizeGraphic() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the top level panel that the plot scale resizing components sit on.
- resno - Static variable in class org.jmol.script.Token
-
- RESOURCES - Static variable in class etomica.graph.view.rasterizer.Messages
-
The error messages bundle class name.
- restartAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- resume - Static variable in class org.jmol.script.Token
-
- retainAll(Collection<?>) - Method in class etomica.graph.model.GraphList
-
- returnMu - Variable in class etomica.normalmode.DataSourcePMu
-
- ReturnValue(int, ISpace) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- reverse(double[], double) - Static method in class etomica.util.SineTransform
-
- reverse - Static variable in class org.jmol.script.Token
-
- reverseCollisionHandler - Variable in class etomica.integrator.IntegratorHard
-
- ReverseOsmosis - Class in etomica.modules.rosmosis
-
Reverse osmosis simulation, based on simulation code by Sohail Murad.
- ReverseOsmosis(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosis
-
- ReverseOsmosisGraphic - Class in etomica.modules.rosmosis
-
Graphical and data collection bits for reverse osmosis simulation.
- ReverseOsmosisGraphic(ReverseOsmosis, Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- ReverseOsmosisGraphic.Applet - Class in etomica.modules.rosmosis
-
- ReverseOsmosisGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
-
- ReverseOsmosisGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
-
- ReverseOsmosisGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWater - Class in etomica.modules.rosmosis
-
Reverse osmosis simulation, based on simulation code by Sohail Murad.
- ReverseOsmosisWater(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWater
-
- ReverseOsmosisWaterGraphic - Class in etomica.modules.rosmosis
-
Graphical and data collection bits for reverse osmosis simulation.
- ReverseOsmosisWaterGraphic(ReverseOsmosisWater) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- ReverseOsmosisWaterGraphic.Applet - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.ModifierSoluteCharge - Class in etomica.modules.rosmosis
-
- revertDiagram() - Method in class etomica.virial.ClusterSumStickyEF
-
set the diagram used for calculating the value to the ith diagram.
- revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- revertF() - Method in class etomica.virial.ClusterTree
-
- rewind - Static variable in class org.jmol.script.Token
-
- rFill(StringXBuilder, String, String) - Static method in class org.jmol.util.TextFormat
-
- rfit - Static variable in class etomica.potential.P2O2Bartolomei
-
- rfit0 - Static variable in class etomica.potential.P2O2Bartolomei
-
- rfitMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- rfitPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- rg - Variable in class etomica.modules.droplet.MeterDeformation
-
- rgb(int, int, int) - Static method in class org.jmol.util.ColorUtil
-
- Rgb16 - Class in org.jmol.util
-
- Rgb16() - Constructor for class org.jmol.util.Rgb16
-
- RheologyGraphic - Class in etomica.modules.rheology
-
Module for "Macromolecular dynamics related to rheological properties
through Brownian dynamics simulations", designed by Lewis Wedgewood.
- RheologyGraphic(SimulationRheology) - Constructor for class etomica.modules.rheology.RheologyGraphic
-
- RheologyGraphic.Applet - Class in etomica.modules.rheology
-
- rho - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- rho - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- rho - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- rho - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- rho - Variable in class etomica.util.numerical.B9Optimizer
-
- rho - Variable in class etomica.util.numerical.VirialOptimizer
-
- rho - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- rho - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- rho - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- rho - Variable in class etomica.virial.cluster.VirialDiagrams
-
- rho - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- rho - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rho - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rho0 - Variable in class etomica.meam.ParameterSetMEAM
-
- rho0 - Static variable in class etomica.statmech.HardSphereSolid
-
- rho0 - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rho0 - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- rho1 - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoA - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- rhoA - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoA - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- rhoA - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- rhoA - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- rhoA - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoA - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAB - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- rhoAB - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoAB - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- rhoAB - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoAB - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAB0 - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoABC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoABC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoAC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAlphaTrans - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- rhoB - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- rhoB - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoB - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- rhoB - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- rhoB - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- rhoB - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoB - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoBC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoBC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoBetaTrans - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- rhoC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoc - Static variable in class etomica.modules.adsorption.EOSSW
-
- rhoC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
-
- rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- rhoForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- rhograd - Variable in class etomica.meam.PotentialCuLREP
-
- rhograd - Variable in class etomica.meam.PotentialEFS
-
- rhograd - Variable in class etomica.meam.PotentialFeEAM
-
- rhograd - Variable in class etomica.meam.PotentialFeEAM_LS
-
- rhoi(IAtomList) - Method in class etomica.meam.PotentialMEAM
-
- rhoi1sq() - Method in class etomica.meam.PotentialMEAM
-
- rhoi2sq() - Method in class etomica.meam.PotentialMEAM
-
- rhoi3sq() - Method in class etomica.meam.PotentialMEAM
-
- RHOj0 - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj1x - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj1y - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj1z - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2 - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2xx - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2xy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2xz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2yy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2yz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2zz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xxx - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xxy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xxz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xyy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xyz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xzz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3yyy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3yyz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3yzz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3zzz - Static variable in class etomica.meam.PotentialMEAM
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- rHSCore - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- ri - Variable in class etomica.models.co2.P2CO2Hellmann
-
- ri - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- ri - Variable in class etomica.potential.P3Induction
-
- ribbon - Static variable in class org.jmol.script.Token
-
- ribbonaspectratio - Static variable in class org.jmol.script.Token
-
- ribbonborder - Static variable in class org.jmol.script.Token
-
- RIGHT - Static variable in class etomica.graphics.DisplayBox
-
- RIGHT - Static variable in class etomica.graphics.DisplayPolytope
-
- RIGHT - Static variable in class etomica.util.Constants.Direction
-
- right - Static variable in class org.jmol.script.Token
-
- rightAngle - Static variable in class etomica.lattice.crystal.Primitive
-
- rightDifference(Quaternion) - Method in class org.jmol.util.Quaternion
-
- rij - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- rij - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- rij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- Rij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- rij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- Rij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- rij - Variable in class etomica.potential.P3Induction
-
- rijVector - Variable in class etomica.models.co2.PNCO2GCPM
-
- rijVector - Variable in class etomica.models.co2.PNGCPM
-
- rijVector - Variable in class etomica.models.water.PNWaterGCPM
-
- rik - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- rik - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- rik - Variable in class etomica.potential.P3Induction
-
- rIndices - Variable in class etomica.virial.cluster.PermutationIterator
-
- Ring - Class in etomica.virial.cluster
-
- Ring(int) - Constructor for class etomica.virial.cluster.Ring
-
Constructor for Ring.
- ring(int) - Static method in class etomica.virial.cluster.Standard
-
Returns a ring of bonds, {{0,1},{1,2},...{n-2,n-1},{n-1,0}}
- ring0 - Variable in class etomica.virial.simulations.ModifierTPI
-
- ring1 - Variable in class etomica.virial.simulations.ModifierTPI
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- ringFrac - Variable in class etomica.virial.ClusterChainHS
-
- ringFrac - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- ringFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- ringFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- ringHS(int) - Static method in class etomica.virial.cluster.Standard
-
Return integral for ring of hard spheres of size nPoints
- ringResult - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- RingResult() - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
-
- rings - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- rj - Variable in class etomica.models.co2.P2CO2Hellmann
-
- rj - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- rj - Variable in class etomica.potential.P3Induction
-
- rjk - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- rjk - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- rjrj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- rk - Variable in class etomica.potential.P3Induction
-
- rkl - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- rLast - Variable in class etomica.data.meter.MeterMeanSquareDisplacement
-
- rm() - Method in interface etomica.api.IAtomType
-
Returns the reciprocal of the mass, 1.0/mass
- rm() - Method in interface etomica.api.IElement
-
- rm() - Method in class etomica.atom.AtomTypeLeaf
-
- rm() - Method in class etomica.chem.elements.Element
-
- rm - Variable in class etomica.chem.elements.ElementChemical
-
- rm() - Method in class etomica.chem.elements.ElementChemical
-
- rm - Variable in class etomica.chem.elements.ElementSimple
-
- rm() - Method in class etomica.chem.elements.ElementSimple
-
- rMax - Variable in class etomica.data.meter.MeterDihedralAngle
-
- rMax - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- rmax - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- rMaxSafe - Variable in class etomica.nbr.CriterionPositionWall
-
- rMin - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- rMin - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- rMin - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- rMin - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- rMin - Static variable in class etomica.potential.P2O2Bartolomei
-
- rMrLast - Variable in class etomica.integrator.IntegratorVerlet.Agent
-
- rna - Static variable in class org.jmol.script.Token
-
- rocket - Static variable in class org.jmol.script.Token
-
- rocketbarrels - Static variable in class org.jmol.script.Token
-
- rOM - Static variable in class etomica.models.water.ConformationWaterTIP4P
-
- root(int, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The integer root.
- root(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Pulling the r-th root.
- root(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
r-th root.
- rootD(double) - Method in interface etomica.space.ISpace
-
Returns the given value raised to the power 1/D, where D is the dimension of the space.
- rootD(double) - Method in class etomica.space.Space
-
- rootD(double) - Method in class etomica.space1d.Space1D
-
Returns the Dth root of the given value, a^(1/D), where D is the dimension of the space.
- rootD(double) - Method in class etomica.space2d.Space2D
-
Returns the square root of the given value, a^(1/D), which is a^(1/2).
- rootD(double) - Method in class etomica.space3d.Space3D
-
Returns the cube root of the given value, a^(1/D) which is a^(1/3).
- rootDeg(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Compute the order of the root r.
- rootPointsSpecial - Static variable in class etomica.graph.model.impl.MetadataImpl
-
- rot - Variable in class etomica.models.hexane.TestHexane
-
- rot - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- rot - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- rot - Variable in class etomica.models.hexane.TestSetToUHexane
-
- rot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rot0 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- rot0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rot0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rot1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- rot1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rot1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rotate - Variable in class etomica.dimer.IntegratorDimerMin
-
- rotate - Variable in class etomica.dimer.IntegratorDimerRT
-
- rotate - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- rotate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- rotate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- rotate - Static variable in class org.jmol.script.Token
-
- rotate(Matrix4f) - Method in class org.jmol.util.Quadric
-
- rotateBy(double, double, IVector, IVectorMutable) - Static method in class etomica.potential.P2NitrogenHellmann
-
- rotateBy(double) - Method in interface etomica.space2d.IOrientation2D
-
Rotate the orientation by the amount dt (radians) in the
counter-clockwise direction.
- rotateBy(double) - Method in class etomica.space2d.Orientation2D
-
Rotates orientation around the given axis by the given value.
- rotateBy(double, IVector) - Method in interface etomica.space3d.IOrientation3D
-
Rotate the orientation by the amount dt (radians) about the given axis.
- rotateBy(double, IVector) - Method in class etomica.space3d.Orientation3D
-
Rotates orientation by the given value about the given axis.
- rotateBy(double, IVector) - Method in class etomica.space3d.OrientationFull3D
-
Rotates orientation by the given value about the given axis.
- rotateByX(float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the x axis
- rotateByXY(float, float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the x and y axes
- rotateByY(float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the y axis
- rotateByZ(float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the z axis
- rotateDimerNewton() - Method in class etomica.dimer.IntegratorDimerMin
-
Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest
curvature mode.
- rotateDimerNewton() - Method in class etomica.dimer.IntegratorDimerRT
-
Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest
curvature mode.
- rotateMolecule - Variable in class etomica.AlkaneEH.CH4NVT
-
- rotateMolecule - Variable in class etomica.AlkaneEH.DHS_NVT
-
- rotateMolecule - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- rotateMolecule - Variable in class etomica.dielectric.DHS_NVT
-
- rotateMolecule - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- rotateMolecule - Variable in class etomica.dielectric.TIP4P_NVT
-
- rotateOrientation(OrientationFull3D) - Method in class etomica.math.Quaternion
-
Rotates the input orientation by using the Quaternion rotation operator L(v) = qvq*.
- rotatePhi - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- rotateTensor - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- rotateTensor - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- rotateToHome() - Method in class g3dsys.control.G3DSys
-
Remove all rotation (and translation) and return to the home position
- rotateToX(float) - Method in class g3dsys.control.TransformManager
-
- rotateToY(float) - Method in class g3dsys.control.TransformManager
-
- rotateToZ(float) - Method in class g3dsys.control.TransformManager
-
- rotateVector(IVectorMutable) - Method in class etomica.math.Quaternion
-
Rotates the input vector by using the Quaternion rotation operator L(v) = qvq*.
- rotation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rotation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- rotation - Variable in class etomica.models.nitrogen.TestRotationVector
-
- rotation - Static variable in class org.jmol.script.Token
-
- rotationAxis - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- rotationAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rotationAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- rotationAxis - Variable in class etomica.models.nitrogen.TestRotationVector
-
- rotationAxis - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- rotationAxis - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- rotationL - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- rotationM - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- rotationN - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- rotationradius - Static variable in class org.jmol.script.Token
-
- rotationTensor - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- rotationTensor - Variable in class etomica.association.BiasVolumeAceticAcid
-
- rotationTensor - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- rotationTensor - Variable in class etomica.association.MCMoveDimerRotate
-
- rotationTensor - Variable in class etomica.association.MCMoveSmerRotate
-
- rotationTensor - Variable in class etomica.data.meter.MeterKineticEnergyRigid
-
- rotationTensor - Variable in class etomica.integrator.IntegratorRigidIterative
-
- rotationTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- rotationTensor - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- rotationTensor - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- rotationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- rotationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- rotationTensor - Variable in class etomica.models.water.OrientationCalcWater3P
-
- rotationTensor - Variable in class etomica.models.water.OrientationCalcWater4P
-
- rotationTensor - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- rotationTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- RotationTensor - Interface in etomica.space
-
A tensor intended for use to define rotations in space.
- rotationTensor - Variable in class etomica.space3d.OrientationFull3D
-
- RotationTensor2D - Class in etomica.space2d
-
- RotationTensor2D() - Constructor for class etomica.space2d.RotationTensor2D
-
- rotationTensor3D - Variable in class etomica.models.water.P2Water4PSoft
-
- RotationTensor3D - Class in etomica.space3d
-
- RotationTensor3D() - Constructor for class etomica.space3d.RotationTensor3D
-
- rotationTolerance - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- rotCounter - Variable in class etomica.dimer.IntegratorDimerMin
-
- rotCounter - Variable in class etomica.dimer.IntegratorDimerRT
-
- rotDim - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- rotNum - Variable in class etomica.dimer.IntegratorDimerRT
-
- rotX(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a rotation matrix about the x axis by the
passed angle.
- rotX(float) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a rotation matrix about the x axis by the
passed angle.
- rotY(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a rotation matrix about the y axis by the
passed angle.
- rotY(float) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a rotation matrix about the y axis by the
passed angle.
- rotZ(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a rotation matrix about the z axis by the
passed angle.
- rotZ(float) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a rotation matrix about the z axis by the
passed angle.
- round(double) - Static method in class etomica.util.FastFourierTransform
-
- roundInt(int) - Static method in class org.jmol.util.GData
-
JavaScript won't really have an integer here after integer division.
- route - Variable in class etomica.action.IntegratorDimerApproach
-
- routeParams - Variable in class etomica.action.IntegratorDimerApproach
-
- rowHeaders - Variable in class etomica.data.types.DataTable.DataInfoTable
-
- rowHeaders - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
-
- rowLabelColumnHeader - Variable in class etomica.graphics.DisplayTable
-
- rowLabels - Variable in class etomica.graphics.DisplayTable
-
- rp - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
-
- rPermutations - Variable in class etomica.virial.ClusterBonds
-
- Rpol - Variable in class etomica.models.water.P2WaterSzalewicz
-
- Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- rPow - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
-
- rPow - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- rPow - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- rPow - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- rr - Variable in class etomica.potential.P2HydrogenPatkowski
-
- rr - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- rr0Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rr0Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rr0Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rr0Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rr1Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rr1Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rr1Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rr1Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rRand - Variable in class etomica.normalmode.MCMoveHarmonic
-
- rrlong - Variable in class etomica.potential.P2HydrogenPatkowski
-
- rrlong - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- rrounded - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- rScale - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- rScale - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- rScaled - Variable in class org.jmol.util.Rgb16
-
- rTensor0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rTensor0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rTensor0 - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rTensor0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rTensor1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rTensor1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rTensor1 - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rTensor1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rTmp - Variable in class etomica.models.water.P2WaterSzalewicz
-
- rTrial - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- rTrial - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- rTrial - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- run() - Method in class etomica.action.activity.ActivityGroupParallel
-
- run() - Method in class etomica.action.activity.ActivityGroupSeries
-
Causes uncompleted actions added to this group to be run in sequence.
- run() - Method in class etomica.action.activity.ActivityIntegrate
-
Main loop for conduct of integration.
- run() - Method in class etomica.action.activity.Controller
-
Causes uncompleted actions added to this group to be run in sequence.
- run() - Method in class etomica.action.Activity
-
Method defining the behavior of the activity.
- run(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- run() - Method in class etomica.graph.engine.Launcher.ConsoleWindowRunnable
-
- run() - Method in class etomica.threaded.atom.PotentialMasterListWorker
-
- run() - Method in class etomica.threaded.domain.PotentialMasterListWorker
-
- run() - Method in class etomica.threads.ThreadsMD
-
- run() - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- run() - Method in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- run() - Method in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- runEmul() - Method in class etomica.potential.PotentialEmul
-
- rungeKutta4(int, double, OdeSolver.Variables, OdeSolver.Rhs) - Static method in class etomica.util.OdeSolver
-
Performs Runge-Kutta integration for fixed number of constant-sized steps.
- rungeKuttaAdaptive(OdeSolver.Variables, double, double, OdeSolver.Rhs) - Static method in class etomica.util.OdeSolver
-
Runge-Kutta integration using an adaptive step-size.
- runGraphic(SimulationVirialOverlap2, int, DisplayTextBox, DisplayTextBox, IAction) - Method in class etomica.virial.GUI.components.SimulationRunner
-
- runit() - Method in class etomica.models.hexane.TestSetToUHexane
-
- runMD() - Method in class etomica.threads.AtomDecompositionMD
-
- runName - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- runName - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
-
- runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- runName - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
-
- running - Variable in class etomica.modules.clustergenerator.MyApplet
-
- runQChem() - Method in class etomica.potential.P2QChem
-
- runSimulation(ModelSimulationEnvironment, ArrayList<ICollectionPotential>) - Method in class etomica.virial.GUI.components.SimulationRunner
-
- runVirial(VirialExternalFieldConfinedOverlap.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
-
- runVirial(VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
-
- runVirial(VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
-
- runVirial(VirialExternalFieldOverlapRho.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldOverlapRho
-
- runVirial(VirialLJ.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJ
-
- runVirial(VirialLJSeries.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJSeries
-
- runVirial(VirialSW.VirialSWParam) - Static method in class etomica.virial.simulations.VirialSW
-
- rv - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- rv - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- Rvdw - Static variable in class etomica.potential.P2QChemInterpolated
-
- RvdwF - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
-
- RvdwF - Variable in class etomica.potential.P2QChemInterpolated
-
- RvdwF - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- RvdwF - Variable in class etomica.potential.P3QChem.DampingParams
-
- RYDBERG_R - Static variable in class etomica.util.Constants
-
Rydberg's constant, in Angstroms.
- rzero - Variable in class etomica.dimer.P1LepsHarmonic
-
- S - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- s - Static variable in class etomica.models.water.P2WaterTIP4P
-
- s - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- s - Static variable in class etomica.potential.P2O2Bartolomei
-
- s - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- s - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- s - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- s - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- s - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- s - Variable in class g3dsys.images.Line
-
- S1DHR(int, double, int) - Static method in class etomica.normalmode.NormalModes1DHR
-
Returns the analytical result for the S matrix (just a scalar in this
case) for the 1D HR system with PBC
- S2 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- S2fit(double, double, double, double, double, double, double) - Method in class etomica.models.water.P2WaterSzalewicz
-
- S3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- sa - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- saa - Static variable in class etomica.potential.P2O2Bartolomei
-
- saaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- saaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- saddle - Variable in class etomica.dimer.IntegratorDimerMin
-
- saddle - Variable in class etomica.dimer.SimDimerLJadatom
-
- saddle - Variable in class etomica.dimer.SimDimerLJgb
-
- saddle - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- saddle - Variable in class etomica.dimer.SimDimerMEAMGB
-
- saddleEnergy - Variable in class etomica.dimer.IntegratorDimerRT
-
- saddleFine - Variable in class etomica.dimer.SimDimerLJadatom
-
- saddleFound - Variable in class etomica.dimer.IntegratorDimerRT
-
- saddleT - Variable in class etomica.dimer.IntegratorDimerRT
-
- safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.AbstractOptionHandler
-
- safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
-
- safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
-
- safetl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- safeTruncate(float, int) - Static method in class org.jmol.util.TextFormat
-
- safetyFactor - Variable in class etomica.nbr.CriterionPositionWall
-
- safetyFactor - Variable in class etomica.nbr.CriterionSimple
-
- safetyFactor - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- sajmols - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajp1 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajpn - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- Sam - Class in etomica.modules.sam
-
Self-assembled monolayer module.
- Sam() - Constructor for class etomica.modules.sam.Sam
-
- SamGraphic - Class in etomica.modules.sam
-
- SamGraphic(Sam) - Constructor for class etomica.modules.sam.SamGraphic
-
- SamGraphic.ActionMoveWall - Class in etomica.modules.sam
-
- SamGraphic.Applet - Class in etomica.modules.sam
-
- SamGraphic.DataPipeStressStrain - Class in etomica.modules.sam
-
- SamGraphic.ModifierWallPosition - Class in etomica.modules.sam
-
- sampleCluster - Variable in class etomica.virial.BoxCluster
-
- sampleCluster - Variable in class etomica.virial.simulations.SimulationVirial
-
- sampleCluster - Variable in class etomica.virial.simulations.SimulationVirialPT
-
- sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- sampleCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- sampleCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- sampleCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- sanityCheckBC - Variable in class etomica.data.AccumulatorAverageFixed
-
- sasurface - Static variable in class org.jmol.script.Token
-
- satisfies(Requirement) - Method in class etomica.compatibility.FeatureSet
-
- save(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- save - Static variable in class org.jmol.script.Token
-
- savedSeed - Variable in class etomica.util.RandomMersenneTwister
-
- savedSeedArray - Variable in class etomica.util.RandomMersenneTwister
-
- saveproteinstructurestate - Static variable in class org.jmol.script.Token
-
- saveValues - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- sb - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- sbet - Static variable in class etomica.potential.P2O2Bartolomei
-
- sbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sBOType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- scale - Variable in class etomica.graphics.DisplayBox
-
Factor used to scale the size of the image.
- scale - Variable in class etomica.graphics.DisplayPolytope
-
Factor used to scale the size of the image.
- scale - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- scale - Variable in class etomica.virial.MCMoveClusterRingScale
-
- scale - Variable in class org.jmol.util.Quadric
-
- scale(float) - Method in class org.jmol.util.Quadric
-
- scale(float) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the scalar multiplication of itself.
- scale(float) - Method in class org.jmol.util.Tuple4f
-
Sets the value of this tuple to the scalar multiplication of itself.
- scaleAdd(float, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the scalar multiplication of itself and
then adds tuple t1 (this = s*this + t1).
- scaleAdd(int, Tuple3i, Tuple3i) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to the scalar multiplication of tuple t1 plus
tuple t2 (this = s*t1 + t2).
- scaleAdd2(float, Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the scalar multiplication of tuple t1 and
then adds tuple t2 (this = s*t1 + t2).
- scaleangstromsperinch - Static variable in class org.jmol.script.Token
-
- scaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociated
-
- scaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- scaleBox(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
-
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicBcc
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicDiamond
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicFcc
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicSimple
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeHcp
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeOrthorhombicHexagonal
-
Rescales the lattice by the given factor.
- scaleFitToScreen() - Method in class g3dsys.control.G3DSys
-
- scaleMomenta() - Method in class etomica.integrator.IntegratorHard
-
Updates collision times appropriately after scaling momenta.
- scaleMomenta() - Method in class etomica.integrator.IntegratorMD
-
Crude method to enforce constant-temperature constraint
Scales momenta of all atoms by a constant factor so that
box adheres to setpoint temperature.
- scaleMomenta(IVector) - Method in class etomica.integrator.IntegratorMD
-
- scaleMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
-
- scaleMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- scaleMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- scalePixelsPerAngstrom - Variable in class g3dsys.control.TransformManager
-
- scalePrec(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Append decimal zeros to the value.
- scalePrec(BigComplex, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Append decimal zeros to the value.
- scalePrec(BigDecimal, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Boost the precision by appending decimal zeros to the value.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvas1D
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvas2D
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSize(double) - Method in class etomica.lattice.crystal.Primitive
-
Scales (multiplies) the size of each primitive vector by the given value.
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveBcc
-
Multiplies the size of the current vectors by the given value.
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveFcc
-
Multiplies the size of the current vectors by the given value.
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveGeneral
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- scaleSize(double) - Method in class etomica.models.hexane.PrimitiveHexane
-
- scaleSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- scaleVector - Variable in class etomica.action.BoxInflate
-
- scaleVector - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- scaleVector - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- scaling - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- scaling - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- scBeads - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- scf - Variable in class etomica.potential.P2QChemInterpolated
-
- scf - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizable
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- ScientificFormat - Class in etomica.util
-
a formatter that uses a format suitable for numeric values in a
scientific context.
- ScientificFormat() - Constructor for class etomica.util.ScientificFormat
-
Create a ScientificFormat using the default pattern and symbols
for the default locale.
- ScientificFormat(Locale) - Constructor for class etomica.util.ScientificFormat
-
Create a ScientificFormat using the default pattern for the
given locale.
- ScientificFormat(String) - Constructor for class etomica.util.ScientificFormat
-
Creates a ScientificFormat using a given pattern
- ScientificFormat(Locale, String) - Constructor for class etomica.util.ScientificFormat
-
Creates a ScientificFormat using a given pattern for the specified
locale
- scoreGreaterThan(int[]) - Method in class etomica.virial.cluster.ClusterDiagram
-
Determines if the cluster's current configuration has a score greater
than the given score.
- screenDiameter - Variable in class org.jmol.util.Point3fi
-
- screened - Variable in class etomica.virial.ClusterWheatleyHS
-
- screened - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- screenSpace(Point3f, Point3i) - Method in class g3dsys.control.G3DSys
-
Converts molspace point p (in Angstroms) to a point on the display
in pixels.
- screenx - Static variable in class org.jmol.script.Token
-
- screenX - Variable in class org.jmol.util.Point3fi
-
- screenxyz - Static variable in class org.jmol.script.Token
-
- screeny - Static variable in class org.jmol.script.Token
-
- screenY - Variable in class org.jmol.util.Point3fi
-
- screenz - Static variable in class org.jmol.script.Token
-
- screenZ - Variable in class org.jmol.util.Point3fi
-
- SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JmolConstants
-
- scriptCommand - Static variable in class org.jmol.script.Token
-
- scriptqueue - Static variable in class org.jmol.script.Token
-
- scriptreportinglevel - Static variable in class org.jmol.script.Token
-
- ScriptVariable - Class in org.jmol.script
-
- ScriptVariable(int) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable.Sort - Class in org.jmol.script
-
- ScriptVariableInt - Class in org.jmol.script
-
- ScriptVariableInt(int) - Constructor for class org.jmol.script.ScriptVariableInt
-
- SearchState - Interface in etomica.graph.isomorphism
-
- secDerXr - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- secDerXr - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- Second - Class in etomica.units
-
- secondaryBox - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- secondaryBox - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- secondaryCoordDef - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- secondaryCoordDef - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- secondaryDirection - Variable in class etomica.config.ConfigurationOrientedFile
-
- secondaryDirection - Variable in class etomica.space3d.OrientationFull3D
-
- secondAxis - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- secondAxis - Variable in class etomica.association.BiasVolumeAceticAcid
-
- secondBox - Variable in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- secondder - Variable in class etomica.meam.PotentialCuLREP
-
- secondder(IAtomList) - Method in class etomica.meam.PotentialCuLREP
-
- secondder - Variable in class etomica.meam.PotentialEFS
-
- secondder(IAtomList) - Method in class etomica.meam.PotentialEFS
-
- secondder - Variable in class etomica.meam.PotentialFeEAM
-
- secondder(IAtomList) - Method in class etomica.meam.PotentialFeEAM
-
- secondder - Variable in class etomica.meam.PotentialFeEAM_LS
-
- secondDerivative(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- secondDerivative - Variable in class etomica.models.water.P2Water4PSoft
-
- secondDerivative(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
-
- secondDerivative - Variable in class etomica.potential.EwaldSummation
-
- secondDerivative(IAtom, IAtom) - Method in class etomica.potential.EwaldSummation
-
- secondDerivative(IMoleculeList) - Method in interface etomica.potential.IPotentialMolecularSecondDerivative
-
- secondDerivative - Variable in class etomica.potential.P2HSDipole
-
- secondDerivative(IMoleculeList) - Method in class etomica.potential.P2HSDipole
-
- secondDerivative - Variable in class etomica.potential.P2LJDipole
-
- secondDerivative(IMoleculeList) - Method in class etomica.potential.P2LJDipole
-
- secondDerivative - Variable in class etomica.potential.P2ReactionFieldDipole
-
- secondDerivative(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
-
- secondDerivativeSum - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- secondDerivativeSum - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- secondDerivativeXr(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- secondDerivativeXrRotRot(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- securityOff - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Controls whether scripts should be run securely or not
- seed - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
-
- SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
-
- seeds - Variable in class etomica.simulation.Simulation
-
- seen(byte) - Method in class etomica.graph.traversal.AbstractTraversal
-
- seenAll() - Method in class etomica.graph.traversal.AbstractTraversal
-
- seenArrays - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- seenParams - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- segment - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- segmentList - Variable in class etomica.graph.property.FFTDecomposition
-
- selectallmodels - Static variable in class org.jmol.script.Token
-
- selected - Static variable in class org.jmol.script.Token
-
- selectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- selectedfloat - Static variable in class org.jmol.script.Token
-
- selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- selecthetero - Static variable in class org.jmol.script.Token
-
- selecthydrogen - Static variable in class org.jmol.script.Token
-
- selectionForKey(char, ComboBoxModel) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Implementation of KeySelectionManager interface that uses key press to
select a unit prefix (instead of selecting a combo box item).
- selectionhalos - Static variable in class org.jmol.script.Token
-
- selectItemTok(Token) - Static method in class org.jmol.script.ScriptVariable
-
- selectItemTok(Token, int) - Static method in class org.jmol.script.ScriptVariable
-
- selectItemVar(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- selectItemVar2(ScriptVariable, int) - Static method in class org.jmol.script.ScriptVariable
-
- selectMolecules() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- selectMolecules() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- selectMolecules() - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- selectMove() - Method in class etomica.integrator.mcmove.MCMoveManager
-
Selects a MCMove instance from among those added to the integrator, with
probability in proportion to the frequency value assigned to the move.
- selfELJ - Static variable in class etomica.models.clathrates.MinimizationTIP4P
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- sep - Variable in class etomica.models.water.P2WaterSzalewicz
-
- separationProbability(int, double) - Static method in class etomica.virial.MCMoveClusterAtomHSRing
-
Normalized probability for the separation of the centers of two spheres located at the
end of a chain of (n+1) overlapping spheres.
- seq - Variable in class etomica.virial.MCMoveClusterAtomHSChain
-
- seq - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- seq - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- sequence - Static variable in class org.jmol.script.Token
-
- serial - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- serialVersionUID - Static variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- serialVersionUID - Static variable in class etomica.models.rowley.DimerApproach
-
- set(int, IAtom) - Method in class etomica.atom.AtomArrayList
-
- set(int, IMolecule) - Method in class etomica.atom.MoleculeArrayList
-
- set(Parser.CommandPropertyValue) - Method in class etomica.graph.engine.Interpreter
-
- set(int, Object) - Method in class etomica.util.ObjectArrayList
-
Replaces the element at the specified position in this list with
the specified element.
- set(int, Rational) - Method in class etomica.veos.bigdecimal.Bernoulli
-
Set a coefficient in the internal table.
- set(int, BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Set a polynomial coefficient.
- set(int, int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Set a polynomial coefficient.
- set(int) - Method in class etomica.veos.bigdecimal.Euler
-
Compute a coefficient in the internal table.
- set(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptVariable
-
creates a NEW version of the variable
- set(int) - Method in class org.jmol.util.BitSet
-
Sets the bit at the specified index to true.
- set(Quaternion) - Method in class org.jmol.util.Quaternion
-
- set(float, float, float) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the specified xyz coordinates.
- set(int, int, int) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to to the specified x, y, and z coordinates.
- set(float, float, float, float) - Method in class org.jmol.util.Tuple4f
-
Sets the value of this tuple to the specified xyzw coordinates.
- set2(Point3f, Point3i) - Static method in class org.jmol.util.Point3fi
-
- set4(float, float, float, float) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this axis angle to the specified x,y,z,angle.
- set_sites(IVector[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- set_sites_itypea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- set_sites_sa - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- set_sites_sitea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- setA(double) - Method in class etomica.models.hexane.PrimitiveHexane
-
Sets A and scales B and C to maintain relative size
- setA(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setA(double) - Method in class etomica.potential.P2Exp6
-
- setA(int, double) - Method in class etomica.potential.P2HeSimplified
-
Sets the ith parameter value
u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X
where X = 10 if useC10 is true, X=8 otherwise
- setA(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setA(double) - Method in class etomica.potential.P2Morse
-
- setA() - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setA() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setA(float[]) - Method in class org.jmol.util.Matrix3f
-
Sets the values in this Matrix3f equal to the row-major array parameter
(ie, the first four elements of the array will be copied into the first row
of this matrix, etc.).
- setA(float[]) - Method in class org.jmol.util.Matrix4f
-
Sets the values in this Matrix4f equal to the row-major array parameter
(ie, the first four elements of the array will be copied into the first row
of this matrix, etc.).
- setA(float[]) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple from the 3 values specified in the array.
- setAA(AxisAngle4f) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this axis angle to the value of axis angle t1.
- setAA(AxisAngle4f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the matrix conversion of the single
precision axis and angle argument.
- setAA(AxisAngle4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the matrix conversion of the single
precision axis and angle argument.
- setAA(AxisAngle4f) - Method in class org.jmol.util.Quaternion
-
- setABC(int) - Method in class org.jmol.util.MeshSurface
-
- setAcceptanceTarget(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets the desired rate of acceptance (as a fraction between 0 and 1
inclusive) of trials of this move.
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- setAccumulator(AccumulatorAverage) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
Specifies the accumulator that generates the displayed values.
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorVar
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlap
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapLJ
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- setAccumulator(IDataSink) - Method in class etomica.virial.simulations.SimulationVirial
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setAccumulator(int, DataAccumulator) - Method in class etomica.virial.simulations.SimulationVirialPT
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirial
-
- setAccumulatorBlockSize(int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setAccumulators(AccumulatorAverageCollapsingLog[]) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- setAccumulatorUpdateInterval(int) - Method in class etomica.data.DataTableAverages
-
Sets the interval for updates to the accumulators feeding this table.
- setAction(IAction) - Method in class etomica.graphics.DeviceButton
-
Defines the action to be performed when the button is pressed.
- setAction(IntegratorAnalytic.AtomTimeAction) - Method in class etomica.integrator.IntegratorAnalytic
-
- setAction(IAction) - Method in class etomica.zeolite.DeviceButtonSingle
-
Defines the action to be performed when the button is pressed.
- setActions(IAction[]) - Method in class etomica.action.activity.ActivityGroupParallel
-
- setActive(boolean) - Method in class etomica.data.DataAccumulator
-
Sets whether accumulation is to be performed in response to interval events.
- setActive(int, boolean, boolean) - Method in class etomica.potential.P1HardBoundary
-
- setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
-
Changes the activation state for a logging level.
- setActivityIntegrate(ActivityIntegrate) - Method in class etomica.dimer.IntegratorDimerMin
-
- setActivityIntegrate(ActivityIntegrate) - Method in class etomica.dimer.IntegratorDimerRT
-
- setAddAnotherSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddPotential(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddPotential(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setAddSameSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies1(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies2(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies3(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAdiabatic() - Method in class etomica.graphics.DeviceThermoSlider
-
Set the Adiabatic button to its selected state.
- setAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the Adiabatic button to its selected state.
- setAdjustInterval(long) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets the interval between steps size adjustments.
- setAdjustInterval(long) - Method in class etomica.overlap.IntegratorOverlap
-
Sets how frequently the appropriate reference vs.
- setAdjustStepFraction(boolean) - Method in class etomica.overlap.IntegratorOverlap
-
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
- setAdjustStepFreq(boolean) - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
- setAdjustStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets the step adjustment size.
- setAelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setAgent(IAtom, E) - Method in class etomica.atom.AtomLeafAgentManager
-
Sets the agent associated with the given atom to be the given agent.
- setAgent(IAtomType, Object) - Method in class etomica.atom.AtomTypeAgentManager
-
Sets the agent associated with the given atom type to be the given
agent.
- setAgent(IMolecule, Object) - Method in class etomica.atom.MoleculeAgentManager
-
Sets the agent associated with the given atom to be the given agent.
- setAgent(ISpecies, Object) - Method in class etomica.atom.SpeciesAgentManager
-
Sets the agent associated with the given atom type to be the given
agent.
- setAgent(IBox, E) - Method in class etomica.box.BoxAgentManager
-
- setAgentManager(AtomLeafAgentManager<IntegratorHard.Agent>) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
- setAgentManager(AtomLeafAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- setAgentManager(AtomLeafAgentManager<AtomPotentialList>) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- setAgentManager(AtomLeafAgentManager<? extends Integrator.Forcible>) - Method in class etomica.potential.PotentialCalculationForceSum
-
- setAgentManager(AtomLeafAgentManager) - Method in class etomica.potential.PotentialCalculationTorqueSum
-
- setAgentManager(AtomLeafAgentManager<? extends Integrator.Forcible>) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- setAggressiveAdjustStepFraction(boolean) - Method in class etomica.overlap.IntegratorOverlap
-
Sets whether to use "aggressive" adjustment.
- setAlertMessage(String) - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- setAlertMsgBoxController(ControllerAlertMsgBox) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- setAlertMsgBoxSpeciesRemoval(ViewAlertMsgBoxSpeciesRemoval) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setAlign(int, int) - Method in class etomica.graphics.DisplayBox
-
- setAlign(int, int) - Method in class etomica.graphics.DisplayPolytope
-
- setAlkaneIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setAlkaneIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setAlkaneLength(int, int) - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
-
- setAlkaneLengthSelectionDM(ModelAlkaneLengthSelection) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- setAlkaneLengthSelectionView(ViewAlkaneLengthSelection, int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- setAll(int) - Static method in class org.jmol.util.BitSetUtil
-
- setAllEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the "All eigenvalues" button to its selected state.
- setAllowedScriptTypes(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the set of allowed script types (i.e., the set of possible
values for the type attribute in the <script> element),
as a comma separated list of allowed values.
- setAllowEqualElements(boolean) - Method in class etomica.lattice.IndexIteratorTriangular
-
Sets flag indicating whether iterates may have elements that are equal to one another.
- setAllPermutations(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to generate all permutations.
- setAllPermutations(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setAllPermutations(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setAllUnits(Unit) - Method in class etomica.graphics.DisplayTable
-
Sets the units of all columns to the given unit.
- setAllWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the "All Wave Vectors" button to its selected state.
- setAlpha(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- setAlpha(double[]) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setAlpha(double[]) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setAlpha(double[], double[]) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
sets the range of parameter values used for Bennets method.
- setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- setAlpha(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- setAlpha(double[]) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setAlpha(double[]) - Method in class etomica.normalmode.MeterTargetTP
-
- setAlpha(double, double) - Method in class etomica.normalmode.SimOverlapModule
-
- setAlpha(double) - Method in class etomica.potential.P2Dreiding
-
- setAlpha(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setAlpha() - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setAlpha() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setAlphaCenter(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- setAlphaEin(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
Sets the Einstein spring constant
u = alpha * r^2
- setAlphaEin(double) - Method in class etomica.normalmode.MCMoveHarmonicEin
-
Sets the Einstein spring constant
- setAlphaFac(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- setAlphaRange(double, double) - Method in class etomica.overlap.MeterOverlap
-
sets the range of parameter values used for Bennets method.
- setAlphaSpan(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setAlphaSpan(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setAlphaSpan(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setAlphaSpan(double) - Method in class etomica.normalmode.MeterTargetTP
-
- setAlternateStylesheet(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the alternateStyleSheet value.
- setAlterSimEnv(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAlterSimEnv(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setAmbientPercent(int) - Static method in class org.jmol.util.GData
-
fractional distance from black for ambient color
- setAmplitude(double) - Method in class etomica.potential.P2Fene
-
- setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
-
- setAngle(int, double) - Method in class etomica.config.ConformationChainLinear
-
- setAngle(int, double) - Method in class etomica.config.ConformationLinear
-
- setAngle(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setAngle(double) - Method in class etomica.potential.P3BondAngle
-
Sets the nominal bond angle (in radians)
- setAngle(double) - Method in class etomica.potential.P3BondAngleDreiding
-
Sets the nominal bond angle (in radians)
- setAngle(double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
Sets the nominal bond angle (in radians)
- setAngleAlpha(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setAngleBeta(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setAngleBeta(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setAngleGamma(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setAngles(double, double, double) - Method in class etomica.action.AtomActionRotateBy
-
- setAngles(double[]) - Method in class etomica.lattice.crystal.Primitive
-
Sets the angles between the primitive vector to the corresponding
values in the given array.
- setAngles(double[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- setAnharmonicConstant(double) - Method in class etomica.potential.P2Anharmonic
-
- setAppending(boolean) - Method in class etomica.data.DataLogger
-
Overwrite or attach the data to the file.
- setApplyToMolecules(boolean) - Method in class etomica.action.BoxImposePbc
-
Sets a flag indicating whether periodic boundaries are applied to the
molecules (true), or to the atoms (false).
- setApproximation(int) - Method in class etomica.virial.cluster.ClusterOperations
-
- setArea(Rectangle2D) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the area as a Rectangle.
- setArray(double[][]) - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
-
- setArrayList(AtomArrayList) - Method in class etomica.atom.AtomToAtomSetFixed
-
- setArrayList(MoleculeArrayList) - Method in class etomica.atom.MoleculeToMoleculeSetFixed
-
- setArrayListPotentialCollection(ArrayList<ICollectionPotential>) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setArrayShape(int[]) - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
-
Sets the array shape.
- setArrayShape(int[]) - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
Sets the array shape.
- setAsCube(double) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Sets the shape of the boundary to a cube with edges equal to the given value.
- setAspect(float) - Method in class g3dsys.images.Ellipse
-
- setAsRectangular(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Sets the shape of the boundary as a rectangular parallelepiped (or
parallelogram) with edge lengths given by the elements of the given
vector.
- setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomDimer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomMonomer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomDimer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomMonomer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomNoSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveBiasUB
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveDimer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveDimerRotate
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeMonomer
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeRotateAssociated
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveRotateAssociated
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveRotateNoSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveSmerRotate
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveVolumeAssociated
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MeterDimerMoleFraction
-
- setAssociationManager(AssociationManagerMolecule) - Method in class etomica.association.MoleculeSourceRandomDimer
-
- setAssociationManager(AssociationManagerMolecule) - Method in class etomica.association.MoleculeSourceRandomMonomer
-
- setAsText(String) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Sets the value, interpreted as being in the editor's units, from a text string.
- setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Sets the first atom for iteration.
- setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Sets the first atom for iteration.
- setAtom(IAtom) - Method in interface etomica.atom.iterator.AtomIteratorAtomDependent
-
- setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
Defines atom returned by iterator and leaves iterator unset.
- setAtom(IAtom) - Method in class etomica.graphics.ColorSchemeNeighbor
-
- setAtom(IAtom) - Method in class etomica.graphics.ColorSchemeNeighborCell
-
- setAtom(IAtom) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
sets the atom whose collision time is to be calculated
- setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- setAtom(IAtom) - Method in class etomica.nbr.site.AtomSite
-
- setAtomAgentManager(IBox, AtomLeafAgentManager<? extends IVector>) - Method in class etomica.potential.P1HarmonicSite
-
- setAtomFilter(AtomFilter) - Method in class etomica.graphics.DisplayBox
-
Mutator method for the atom filter that determines which atoms
are displayed.
- setAtomInfo(IAtomType, P2SemiclassicalAtomic.AtomInfo) - Method in class etomica.potential.P2SemiclassicalAtomic
-
- setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterElongation
-
- setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterStrain
-
- setAtomPositionDefinition(IAtomPositionDefinition) - Method in class etomica.action.MoleculeActionTranslateTo
-
- setAtomPositionDefinition(IAtomPositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- setAtomPositionDefinition(IAtomPositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- setAtoms(IAtomList) - Method in class etomica.atom.AtomListWrapper
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IAtom[]) - Method in class etomica.atom.AtomsetArray
-
Copies the atoms in the given array to the wrapped, final array of atoms.
- setAtoms(IAtomList) - Method in class etomica.atom.AtomsetArray
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IMoleculeList) - Method in class etomica.atom.MoleculeListWrapper
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IMolecule[]) - Method in class etomica.atom.MoleculesetArray
-
Copies the atoms in the given array to the wrapped, final array of atoms.
- setAtoms(IMoleculeList) - Method in class etomica.atom.MoleculesetArray
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IAtom, IAtom) - Method in class etomica.data.DataSourceAtomDistance
-
- setAtoms(IMoleculeList) - Method in class etomica.data.meter.MeterStructureFactor
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveDimer
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveDimerRotate
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveSmer
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveSmerRotate
-
- setAtomSource(AtomSource) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- setAtomSource(AtomSource) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- setAtomSource(MoleculeSource) - Method in class etomica.models.hexane.MCMoveReptate
-
- setAtomSource(AtomSource) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setAtomSource(AtomSource) - Method in class etomica.virial.MCMoveClusterAtomQ
-
- setAtomType(IAtomType) - Method in class etomica.data.meter.MeterRDF
-
- setAtomType(IAtomType) - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- setAtomTypes(IAtomType, IAtomType) - Method in class etomica.data.meter.MeterRDF
-
- setAtomTypes(int[]) - Method in class etomica.species.SpeciesSpheresCustom
-
- setAutoScale(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
- setAvgDef(boolean) - Method in class etomica.normalmode.DataSourceFE
-
- setAxial(int, double) - Method in interface etomica.space.RotationTensor
-
- setAxial(int, double) - Method in class etomica.space2d.RotationTensor2D
-
- setAxial(int, double) - Method in class etomica.space3d.RotationTensor3D
-
Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by
the given angle.
- setAxisSymmetric(boolean) - Method in class etomica.species.SpeciesSpheresRotating
-
- setB(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setB(double) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setB(double) - Method in class etomica.potential.P2Exp6
-
- setBackgroundArgb(int) - Method in class org.jmol.util.GData
-
sets background color to the specified argb value
- setBackgroundColor(Color) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the backgroundColor value.
- setBackgroundColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the background color of the display box canvas.
- setBackgroundColor(Color) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Sets the background color of the display box canvas.
- setBackgroundImage(Object) - Method in class org.jmol.util.GData
-
- setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
-
- setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setBarrier(double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
Specifies the basis, which identifies the molecules subject to
iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntergroupExchange
-
Specifies the basis, which identifies the molecules subject to
iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntragroupExchange
-
Specifies the basis, which identifies the molecules subject to
iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIndexList
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntergroup
-
Specifies the basis, which identifies the atoms subject to iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntragroup
-
Specifies the parent atom of the iterates.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Sets the basis for iteration, such that the childList atoms of the given
atom will be subject to iteration (within any specifications given by a
prior or subsequent call to setTarget).
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Sets the basis for iteration, such that the childList atoms of the given
atom will be subject to iteration (within any specifications given by a
prior or subsequent call to setTarget).
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- setBasis(IMoleculeList) - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent
-
Identifies the atoms that form the basis for iteration, such that
the childList atoms of those given will form the iterates.
- setBasis(IMoleculeList) - Method in interface etomica.atom.iterator.MoleculesetIteratorBasisDependent
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.TripletInnerSequential
-
- setBasis(IMoleculeList) - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- setBasisMolecules(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setBasisMonoclinic() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setBasisOrthorhombic() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setBasisSurface(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setBbcage(float) - Method in class org.jmol.util.BoxInfo
-
- setBennetParam(double, double) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
sets the range of parameter values used for Bennets method.
- setBennetParam(double, double) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
sets the range of parameter values used for Bennets method.
- setBennetParam(double, double) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
sets the range of parameter values used for Bennets method.
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setBeta(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- setBeta(double) - Method in class etomica.potential.P4TorsionDreiding
-
- setBeta3() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBeta4211() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBeta4220() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBetaPhase(boolean) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setBetaPositionAndOrientation(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setBGColor(Color) - Method in class g3dsys.control.G3DSys
-
Change the background color of the G3D display
- setBiasCubeDimensions(IVector) - Method in class etomica.association.BiasVolumeCube
-
- setBiasCubeDimensions(double) - Method in class etomica.association.BiasVolumeCube
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphere
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphereOriented
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphere
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphereOriented
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- setBiasVolume(BiasVolume2SiteAceticAcid) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- setBiasVolume(BiasVolume2SiteAceticAcid) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- setBinSize(double) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- setBit(int) - Method in interface etomica.graph.model.Bitmap
-
- setBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit
bitSize() - 1 of bitmap.
- setBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
- setBits(boolean) - Method in interface etomica.graph.model.Bitmap
-
- setBits(boolean) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- setBits(boolean) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1).
- setBits(boolean) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- setBits(int, int) - Method in class org.jmol.util.BitSet
-
Sets the bits from the specified fromIndex (inclusive) to the
specified toIndex (exclusive) to true.
- setBitSize(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
- setBitSize(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- setBitTo(int, boolean) - Method in class org.jmol.util.BitSet
-
Sets the bit at the specified index to the specified value.
- setBlockDataSink(IDataSink) - Method in class etomica.data.AccumulatorAverageFixed
-
- setBlockSize(long) - Method in class etomica.data.AccumulatorAverage
-
Sets the size of the block used to group data for error analysis.
- setBlockSize(long) - Method in class etomica.data.AccumulatorAverageCollapsing
-
Sets the size of the block used to group data for error analysis.
- setBondConstraints(ISpecies, int[][], double[]) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setBondDelta(double) - Method in class etomica.potential.P2HardBond
-
Sets the bond extension factor (max = length * (1+delta))
- setBondDelta(double) - Method in class etomica.potential.P2PenetrableBond
-
Sets the bond extension factor (max = length * (1+delta))
- setBonded(boolean) - Method in class etomica.nbr.CriterionBondedSimple
-
- setBonded(boolean, IAtom, IAtom, double) - Method in class etomica.potential.P2HardBondedList
-
Adds/removes the pair of atoms to/from each other's bonded list.
- setBondedSurfaceAtoms(IMolecule, IAtomList) - Method in class etomica.modules.sam.CriterionTether3
-
- setBondFac(double) - Method in class etomica.modules.colloid.P2HardSphereMC
-
- setBondFac(double) - Method in class etomica.modules.colloid.P2SquareWellMonomer
-
- setBondingPotential(Potential2) - Method in class etomica.chem.models.ModelChain
-
Set the bonding potential for adjacent atoms in the chain molecule.
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setBondL(double) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- setBondL(double) - Method in class etomica.virial.SpeciesFactorySpheres2
-
- setBondLength(double) - Method in class etomica.atom.AtomHydrogen
-
- setBondLength(double) - Method in class etomica.config.ConformationChainLinear
-
- setBondLength(double) - Method in class etomica.config.ConformationLinear
-
- setBondLength(double) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- setBondLength(double) - Method in class etomica.potential.P2Dreiding
-
- setBondLength(double) - Method in class etomica.potential.P2HardBond
-
Setter method for the bond length
- setBondLength(double) - Method in class etomica.potential.P2PenetrableBond
-
Setter method for the bond length
- setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setBondLength(double) - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- setBondLength(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setBondLength(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setBondLengths(double[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- setBonds(int[][]) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- setBonds(int[]) - Method in class etomica.virial.cluster.ClusterTreeNode
-
- setBondTheta(double) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- setBondTheta(double) - Method in class etomica.virial.SpeciesFactorySpheres2
-
- setBondType(int) - Method in class etomica.models.water.P2HardAssociationGCPMReference
-
- setBondType(int) - Method in class etomica.models.water.PNWaterGCPMThreeSite
-
- setBondType(int) - Method in class g3dsys.images.Bond
-
- setBoolean(boolean) - Method in class etomica.integrator.IntegratorGear4NPH.EnsembleToggler
-
- setBoolean(boolean) - Method in interface etomica.modifier.ModifierBoolean
-
Sets the modified value to the given boolean.
- setBoolean(boolean) - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
-
- setBorderAlignment(int) - Method in class etomica.graphics.DeviceSlider
-
- setBorderAlignment(int) - Method in class etomica.graphics.DeviceSpinner
-
- setBorderBackground(Color) - Method in class etomica.graphics.DeviceBox
-
- setBoundaries(int, double[], int[]) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setBoundary(IBoundary) - Method in interface etomica.api.IBox
-
Sets the box's boundary to the given IBoundary.
- setBoundary(IBoundary) - Method in class etomica.box.Box
-
- setBoundaryFrameColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the color of the box boundary.
- setBoundaryFrameColor(Color) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Sets the color of the box boundary.
- setBoundaryPadding(double) - Method in class etomica.config.ConfigurationLattice
-
- setBoundaryVectors(double[]) - Method in class g3dsys.control.G3DSys
-
Sets the boundary vectors to be used for calculating image shells
- setBoundaryVectors(double[]) - Method in class g3dsys.images.ImageShell
-
- setBoundaryVectorsIterator(IndexIterator) - Method in class g3dsys.control.G3DSys
-
Sets the index iterator to use for calculating image shells
- setBoundaryVectorsIterator(IndexIterator) - Method in class g3dsys.images.ImageShell
-
- setBoundaryWall(boolean) - Method in class etomica.nbr.CriterionPositionWall
-
Sets whether the walls are at the box boundaries or not.
- setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.util.BoxInfo
-
- setBoundingBox(IVector, IVector) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the display bounding box.
- setBoundingBox(float, float, float, float, float, float) - Method in class g3dsys.control.G3DSys
-
Set the min and maximum coordinates for the model.
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvas1D
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvas2D
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytope
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
- setBounds(int, int, int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- setBox(IBox) - Method in interface etomica.action.BoxAction
-
- setBox(IBox) - Method in class etomica.action.BoxActionAdapter
-
- setBox(IBox) - Method in class etomica.action.BoxQuench
-
- setBox(IBox) - Method in class etomica.action.PDBWriter
-
- setBox(IBox) - Method in class etomica.action.WriteConfiguration
-
Sets the box whose atom coordinates get written to the file.
- setBox(IBox) - Method in class etomica.action.WriteConfigurationBinary
-
Sets the box whose atom coordinates get written to the file.
- setBox(IBox) - Method in class etomica.action.WriteConfigurationDLPOLY
-
Sets the box whose atom coordinates get written to the file.
- setBox(IBox) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Sets the box whose atom coordinates get written to the file.
- setBox(IBox) - Method in interface etomica.api.IBoundary
-
Sets the box that holds the IBoundary.
- setBox(IBox) - Method in interface etomica.api.IPotential
-
Informs the potential of the box on which it acts so that it can
properly consider the boundaries.
- setBox(IBox) - Method in class etomica.association.AtomSourceRandomDimer
-
- setBox(IBox) - Method in class etomica.association.AtomSourceRandomSmer
-
- setBox(IBox) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setBox(IBox) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setBox(IBox) - Method in class etomica.association.BiasVolumeCube
-
- setBox(IBox) - Method in class etomica.association.BiasVolumeSphere
-
- setBox(IBox) - Method in class etomica.association.BiasVolumeSphereOriented
-
- setBox(IBox) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- setBox(IBox) - Method in class etomica.association.MCMoveBiasUB
-
- setBox(IBox) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- setBox(IBox) - Method in class etomica.association.MCMoveDimer
-
- setBox(IBox) - Method in class etomica.association.MCMoveDimerRotate
-
- setBox(IBox) - Method in class etomica.association.MCMoveSmer
-
- setBox(IBox) - Method in class etomica.association.MCMoveSmerRotate
-
- setBox(IBox) - Method in class etomica.association.MCMoveVolumeAssociated
-
- setBox(IBox) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- setBox(IBox) - Method in class etomica.association.MeterDimerMoleFraction
-
- setBox(IBox) - Method in class etomica.association.MoleculeSourceRandomDimer
-
- setBox(IBox) - Method in interface etomica.atom.AtomSource
-
sets the Box the source should pull Atoms from.
- setBox(IBox) - Method in class etomica.atom.AtomSourceRandomLeaf
-
- setBox(IBox) - Method in class etomica.atom.AtomSourceRandomSpecies
-
- setBox(IBox) - Method in class etomica.atom.iterator.ApiLeafAtoms
-
Conditions iterator to return all leaf-atom pairs from the given box.
- setBox(IBox) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Sets the box containing the molecules for iteration.
- setBox(IBox) - Method in class etomica.atom.iterator.AtomIteratorLeafAtoms
-
Configures iterator to form its iterates from the leaf atoms of the given
box.
- setBox(IBox) - Method in interface etomica.atom.iterator.AtomsetIteratorBoxDependent
-
Sets the Box to pull iterates from
- setBox(IBox) - Method in class etomica.atom.iterator.MoleculeIteratorAll
-
Sets the box containing the molecules for iteration.
- setBox(IBox) - Method in class etomica.atom.iterator.MoleculeIteratorAllMolecules
-
Sets the box having the molecules to be returned as iterates.
- setBox(IBox) - Method in class etomica.atom.iterator.MoleculeIteratorMolecule
-
Sets the box containing the molecules for iteration.
- setBox(IBox) - Method in interface etomica.atom.iterator.MoleculesetIteratorBoxDependent
-
Sets the Box to pull iterates from
- setBox(IBox) - Method in class etomica.atom.iterator.MpiInterspecies1A
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(IBox) - Method in class etomica.atom.iterator.MpiInterspeciesAA
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(IBox) - Method in class etomica.atom.iterator.MpiIntraspecies1A
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(IBox) - Method in class etomica.atom.iterator.MpiIntraspeciesAA
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(IBox) - Method in class etomica.atom.iterator.MpiMolecule
-
Specifies the box from which iterates are taken.
- setBox(IBox) - Method in interface etomica.atom.MoleculeSource
-
sets the Box the source should pull Atoms from.
- setBox(IBox) - Method in class etomica.atom.MoleculeSourceRandomMolecule
-
- setBox(IBox) - Method in class etomica.atom.MoleculeToMoleculeListSpecies
-
- setBox(IBox) - Method in interface etomica.box.RandomPositionSource
-
Notifies the RandomPositionSource of the box from which random positions
should be taken from.
- setBox(IBox) - Method in class etomica.box.RandomPositionSourceDeformable
-
- setBox(IBox) - Method in class etomica.box.RandomPositionSourceRectangular
-
- setBox(IBox) - Method in class etomica.data.DataProcessorInterfacialTension
-
- setBox(IBox) - Method in interface etomica.data.DataSourcePositioned
-
- setBox(IBox) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- setBox(IBox) - Method in class etomica.data.meter.MeterAvgBondLength
-
- setBox(IBox) - Method in class etomica.data.meter.MeterBondOrderParameterQ
-
- setBox(IBox) - Method in class etomica.data.meter.MeterDensity
-
- setBox(IBox) - Method in class etomica.data.meter.MeterDihedralAngle
-
- setBox(IBox) - Method in class etomica.data.meter.MeterDipoleSumSquared1site
-
- setBox(IBox) - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
-
- setBox(IBox) - Method in class etomica.data.meter.MeterHyperVirial
-
- setBox(IBox) - Method in class etomica.data.meter.MeterKineticEnergy
-
- setBox(IBox) - Method in class etomica.data.meter.MeterKineticEnergyRigid
-
Sets the box to the given box.
- setBox(IBox) - Method in class etomica.data.meter.MeterMoleFraction
-
- setBox(IBox) - Method in class etomica.data.meter.MeterMomentumCOM
-
- setBox(IBox) - Method in class etomica.data.meter.MeterNMolecules
-
- setBox(IBox) - Method in class etomica.data.meter.MeterPositionCOM
-
- setBox(IBox) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setBox(IBox) - Method in class etomica.data.meter.MeterPressure
-
- setBox(IBox) - Method in class etomica.data.meter.MeterPressureTensor
-
Sets the integrator associated with this instance.
- setBox(IBox) - Method in class etomica.data.meter.MeterProfile
-
- setBox(IBox) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- setBox(IBox) - Method in class etomica.data.meter.MeterProfileByVolume
-
- setBox(IBox) - Method in class etomica.data.meter.MeterRadiusGyration
-
- setBox(IBox) - Method in class etomica.data.meter.MeterRDF
-
- setBox(IBox) - Method in class etomica.data.meter.MeterRDFPC
-
- setBox(IBox) - Method in class etomica.data.meter.MeterTensorVelocity
-
- setBox(IBox) - Method in class etomica.data.meter.MeterVolume
-
- setBox(IBox) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setBox(IBox) - Method in class etomica.data.meter.PotentialCalculationRDF
-
- setBox(IBox) - Method in class etomica.freeenergy.npath.DataSourceEnergies
-
- setBox(IBox) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- setBox(IBox) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- setBox(IBox) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- setBox(IBox) - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- setBox(IBox) - Method in class etomica.graphics.DeviceNSelector
-
- setBox(IBox) - Method in class etomica.graphics.DisplayBox
-
Specifies the box for this display.
- setBox(IBox) - Method in class etomica.integrator.IntegratorBox
-
Performs activities needed to set up integrator to work on given box.
- setBox(IBox) - Method in class etomica.integrator.IntegratorConNVT
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorGear4
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorHard
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorMC
-
Invokes superclass method and informs all MCMoves about the new box.
- setBox(IBox) - Method in class etomica.integrator.IntegratorMD
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setBox(IBox) - Method in class etomica.integrator.IntegratorVerlet
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveBox
-
Sets the box on which this move acts.
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Invokes superclass method and informs all MCMoves about the new box.
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveRotate
-
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Extends the superclass method to initialize the exchange-set species agents for the box.
- setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setBox(IBox) - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- setBox(IBox) - Method in class etomica.liquidLJ.MeterPU
-
- setBox(IBox) - Method in class etomica.liquidLJ.MeterPUCut
-
- setBox(IBox) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setBox(IBox) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setBox(IBox) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setBox(IBox) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- setBox(IBox) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- setBox(IBox) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- setBox(IBox) - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- setBox(IBox) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- setBox(IBox) - Method in class etomica.meam.PotentialCuLREP
-
- setBox(IBox) - Method in class etomica.meam.PotentialEFS
-
- setBox(IBox) - Method in class etomica.meam.PotentialFeEAM
-
- setBox(IBox) - Method in class etomica.meam.PotentialFeEAM_LS
-
- setBox(IBox) - Method in class etomica.meam.PotentialMEAM
-
- setBox(IBox) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- setBox(IBox) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- setBox(IBox) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- setBox(IBox) - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- setBox(IBox) - Method in class etomica.models.co2.P2CO2Hellmann
-
- setBox(IBox) - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- setBox(IBox) - Method in class etomica.models.co2.PNCO2GCPM
-
- setBox(IBox) - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- setBox(IBox) - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
-
- setBox(IBox) - Method in class etomica.models.co2.PNGCPM
-
- setBox(IBox) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- setBox(IBox) - Method in class etomica.models.hexane.MCMoveCBMC
-
- setBox(IBox) - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- setBox(IBox) - Method in class etomica.models.hexane.MCMoveReptate
-
- setBox(IBox) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- setBox(IBox) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- setBox(IBox) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setBox(IBox) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- setBox(IBox) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- setBox(IBox) - Method in class etomica.models.nitrogen.P2NitrogenAB
-
- setBox(IBox) - Method in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- setBox(IBox) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
-
- setBox(IBox) - Method in class etomica.models.nitrogen.PRotConstraint
-
- setBox(IBox) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setBox(IBox) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setBox(IBox) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setBox(IBox) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- setBox(IBox) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- setBox(IBox) - Method in class etomica.models.water.P2Water3P
-
- setBox(IBox) - Method in class etomica.models.water.P2Water4P
-
- setBox(IBox) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- setBox(IBox) - Method in class etomica.models.water.P2WaterSzalewicz
-
- setBox(IBox) - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- setBox(IBox) - Method in class etomica.models.water.PNWaterGCPM
-
- setBox(IBox) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setBox(IBox) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- setBox(IBox) - Method in class etomica.modules.adsorption.MyMCMove
-
- setBox(IBox) - Method in class etomica.modules.adsorption.P1Wall
-
- setBox(IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- setBox(IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- setBox(IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- setBox(IBox) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- setBox(IBox) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- setBox(IBox) - Method in class etomica.modules.colloid.MeterEnd2End
-
- setBox(IBox) - Method in class etomica.modules.colloid.P1Wall
-
- setBox(IBox) - Method in class etomica.modules.dcvgcmd.MeterFlux
-
- setBox(IBox) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- setBox(IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- setBox(IBox) - Method in class etomica.modules.droplet.MeterDeformation
-
- setBox(IBox) - Method in class etomica.modules.droplet.P1Smash
-
- setBox(IBox) - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- setBox(IBox) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- setBox(IBox) - Method in class etomica.modules.entropylottery.MeterEntropy
-
- setBox(IBox) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- setBox(IBox) - Method in class etomica.modules.interfacial.MeterOrientation
-
- setBox(IBox) - Method in class etomica.modules.materialfracture.MeterElongation
-
- setBox(IBox) - Method in class etomica.modules.materialfracture.MeterStrain
-
- setBox(IBox) - Method in class etomica.modules.materialfracture.MeterStress
-
- setBox(IBox) - Method in class etomica.modules.materialfracture.P1Tension
-
- setBox(IBox) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- setBox(IBox) - Method in class etomica.modules.mu.P1MagicWall
-
- setBox(IBox) - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- setBox(IBox) - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
-
- setBox(IBox) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- setBox(IBox) - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- setBox(IBox) - Method in class etomica.modules.rheology.MeterEndToEnd
-
- setBox(IBox) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setBox(IBox) - Method in class etomica.modules.rheology.MeterViscosity
-
- setBox(IBox) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setBox(IBox) - Method in class etomica.modules.sam.CriterionTether3
-
- setBox(IBox) - Method in class etomica.modules.sam.MeterTilt
-
- setBox(IBox) - Method in class etomica.modules.sam.MeterWallPressure
-
- setBox(IBox) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setBox(IBox) - Method in class etomica.modules.vle.MeterPressure2
-
- setBox(IBox) - Method in class etomica.nbr.cell.Api1ACell
-
- setBox(IBox) - Method in class etomica.nbr.cell.AtomIteratorCell
-
- setBox(IBox) - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- setBox(IBox) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- setBox(IBox) - Method in class etomica.nbr.CriterionAdapter
-
Specifies to the wrapped criterion the box where the criterion is being
applied.
- setBox(IBox) - Method in class etomica.nbr.CriterionAll
-
Performs no action.
- setBox(IBox) - Method in class etomica.nbr.CriterionNone
-
Performs no action.
- setBox(IBox) - Method in class etomica.nbr.CriterionPositionWall
-
- setBox(IBox) - Method in class etomica.nbr.CriterionSimple
-
- setBox(IBox) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Specifies to the wrapped criterion the box where the criterion is being
applied.
- setBox(IBox) - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Performs no action.
- setBox(IBox) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setBox(IBox) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
Specifies the box where the criterion is being applied.
- setBox(IBox) - Method in interface etomica.nbr.NeighborCriterion
-
Specifies the box where the criterion is being applied.
- setBox(IBox) - Method in class etomica.nbr.site.Api1ASite
-
- setBox(IBox) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- setBox(IBox) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- setBox(IBox) - Method in class etomica.normalmode.IntegratorHardMDMC
-
- setBox(IBox) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setBox(IBox) - Method in class etomica.normalmode.MCMoveWV
-
- setBox(IBox) - Method in class etomica.normalmode.MeterAPIPotentialEnergy
-
- setBox(IBox) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setBox(IBox) - Method in class etomica.normalmode.MeterNormalMode
-
Sets the box, and should be called while the Atoms are in
their lattice positions.
- setBox(IBox) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setBox(IBox) - Method in class etomica.normalmode.MeterPhiDeviation
-
- setBox(IBox) - Method in class etomica.normalmode.MeterPlaneSlip
-
- setBox(IBox) - Method in class etomica.normalmode.MeterThetaDeviation
-
- setBox(IBox) - Method in class etomica.normalmode.MeterTilt
-
- setBox(IBox) - Method in class etomica.normalmode.MeterTiltHistogram
-
- setBox(IBox) - Method in class etomica.normalmode.MeterTiltRotation
-
- setBox(IBox) - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- setBox(IBox) - Method in class etomica.normalmode.MeterTiltRotationStdev
-
- setBox(IBox) - Method in class etomica.normalmode.P1ConstraintNbr
-
- setBox(IBox) - Method in class etomica.normalmode.P1ConstraintNbrHcp
-
- setBox(IBox) - Method in class etomica.normalmode.P2XOrder
-
- setBox(IBox) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- setBox(IBox) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- setBox(IBox) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setBox(IBox) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setBox(IBox) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setBox(IBox) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setBox(IBox) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- setBox(IBox) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setBox(IBox) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- setBox(IBox) - Method in class etomica.potential.EwaldSummation
-
- setBox(IBox) - Method in class etomica.potential.EwaldSumMolecules
-
- setBox(IBox) - Method in class etomica.potential.P1ExternalField
-
- setBox(IBox) - Method in class etomica.potential.P1HardBoundary
-
- setBox(IBox) - Method in class etomica.potential.P1HarmonicSite
-
- setBox(IBox) - Method in class etomica.potential.P1HydrogenMielke
-
- setBox(IBox) - Method in class etomica.potential.P22CLJQ
-
- setBox(IBox) - Method in class etomica.potential.P2CO2EMP
-
- setBox(IBox) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setBox(IBox) - Method in class etomica.potential.P2DLPOLY
-
- setBox(IBox) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationCone
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeReference
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
- setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeSW
-
- setBox(IBox) - Method in class etomica.potential.P2HardBondedList
-
- setBox(IBox) - Method in class etomica.potential.P2HardWrapper
-
- setBox(IBox) - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- setBox(IBox) - Method in class etomica.potential.P2HePCKLJS.P2HeTI
-
- setBox(IBox) - Method in class etomica.potential.P2HeSimplified.P2HeQFH
-
- setBox(IBox) - Method in class etomica.potential.P2HeSimplified.P2HeTI
-
- setBox(IBox) - Method in class etomica.potential.P2HSDipole
-
- setBox(IBox) - Method in class etomica.potential.P2HydrogenHinde
-
- setBox(IBox) - Method in class etomica.potential.P2HydrogenHindeAtomic
-
- setBox(IBox) - Method in class etomica.potential.P2HydrogenHindePatkowski
-
- setBox(IBox) - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- setBox(IBox) - Method in class etomica.potential.P2HydrogenPatkowski
-
- setBox(IBox) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- setBox(IBox) - Method in class etomica.potential.P2Ideal
-
Does nothing.
- setBox(IBox) - Method in class etomica.potential.P2LJDipole
-
- setBox(IBox) - Method in class etomica.potential.P2LJQ
-
- setBox(IBox) - Method in class etomica.potential.P2LJQQ
-
- setBox(IBox) - Method in class etomica.potential.P2MoleculeMonatomic
-
- setBox(IBox) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- setBox(IBox) - Method in class etomica.potential.P2MoleculeTruncated
-
- setBox(IBox) - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- setBox(IBox) - Method in class etomica.potential.P2NitrogenHellmann
-
- setBox(IBox) - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- setBox(IBox) - Method in class etomica.potential.P2O2Bartolomei
-
- setBox(IBox) - Method in class etomica.potential.P2QChem
-
- setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
-
- setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipole
-
- setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- setBox(IBox) - Method in class etomica.potential.P2SemiclassicalAtomic
-
- setBox(IBox) - Method in class etomica.potential.P2SemiclassicalMolecular
-
- setBox(IBox) - Method in class etomica.potential.P2SoftSphericalTruncated
-
- setBox(IBox) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- setBox(IBox) - Method in class etomica.potential.P2SoftTruncated
-
- setBox(IBox) - Method in class etomica.potential.P2SpheroPolyhedron
-
- setBox(IBox) - Method in class etomica.potential.P2SquareWellRobust
-
- setBox(IBox) - Method in class etomica.potential.P2TriangleWell
-
- setBox(IBox) - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- setBox(IBox) - Method in class etomica.potential.P3AxilrodTeller
-
- setBox(IBox) - Method in class etomica.potential.P3BondAngle
-
- setBox(IBox) - Method in class etomica.potential.P3BondAngleDreiding
-
- setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setBox(IBox) - Method in class etomica.potential.P3HydrogenATM
-
- setBox(IBox) - Method in class etomica.potential.P3HydrogenManzhos
-
- setBox(IBox) - Method in class etomica.potential.P3Induction
-
- setBox(IBox) - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- setBox(IBox) - Method in class etomica.potential.P4BondTorsion
-
- setBox(IBox) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- setBox(IBox) - Method in class etomica.potential.P4TorsionDreiding
-
- setBox(IBox) - Method in class etomica.potential.Potential
-
Informs the potential of the box on which it acts.
- setBox(IBox) - Method in class etomica.potential.Potential0Lrc
-
- setBox(IBox) - Method in class etomica.potential.Potential1
-
- setBox(IBox) - Method in class etomica.potential.Potential2HardSpherical
-
- setBox(IBox) - Method in class etomica.potential.Potential2SoftSpherical
-
- setBox(IBox) - Method in class etomica.potential.Potential2SoftSphericalLS
-
- setBox(IBox) - Method in class etomica.potential.PotentialAtomicSum
-
- setBox(IBox) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- setBox(IBox) - Method in class etomica.potential.PotentialDLPOLY
-
- setBox(IBox) - Method in class etomica.potential.PotentialEmul
-
- setBox(IBox) - Method in class etomica.potential.PotentialGroup
-
- setBox(IBox) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- setBox(IBox) - Method in class etomica.potential.PotentialMolecular
-
Informs the potential of the box on which it acts.
- setBox(IBox) - Method in class etomica.potential.PotentialMolecularMonatomic
-
- setBox(IBox) - Method in class etomica.potential.PotentialMolecularSum
-
- setBox(Box) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- setBox(IBox) - Method in class etomica.rotation.P2LJDipole
-
- setBox(IBox) - Method in class etomica.space.Boundary
-
Sets the boundary's box to be the given box.
- setBox(IBox) - Method in class etomica.spin.MCMoveSpinFlip
-
- setBox(IBox) - Method in class etomica.spin.MeterSpin
-
- setBox(IBox) - Method in class etomica.spin.P2Spin
-
- setBox(IBox) - Method in class etomica.threaded.PotentialThreaded
-
- setBox(IBox) - Method in class etomica.virial.ClusterSumIC.FR2
-
- setBox(BoxCluster) - Method in interface etomica.virial.ClusterWeightSumWall.DataSourceClusterWall
-
- setBox(IBox) - Method in class etomica.virial.MayerD2FDT2Spherical
-
- setBox(IBox) - Method in class etomica.virial.MayerDFDTSpherical
-
- setBox(IBox) - Method in class etomica.virial.MayerDFQFHDTSpherical
-
- setBox(IBox) - Method in class etomica.virial.MayerEGeneral
-
- setBox(IBox) - Method in class etomica.virial.MayerEHardSphere
-
- setBox(IBox) - Method in class etomica.virial.MayerENonGeneral
-
- setBox(IBox) - Method in class etomica.virial.MayerESpherical
-
- setBox(IBox) - Method in interface etomica.virial.MayerFunction
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionMolecularThreeBody
-
- setBox(IBox) - Method in interface etomica.virial.MayerFunctionNonAdditive
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionNonAdditiveFull
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionProductGeneral
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionSphericalThreeBody
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionSum
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionSumGeneral
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionTemperature
-
- setBox(IBox) - Method in class etomica.virial.MayerFunctionThreeBody
-
- setBox(IBox) - Method in class etomica.virial.MayerGeneral
-
- setBox(IBox) - Method in class etomica.virial.MayerGeneralAtomic
-
- setBox(IBox) - Method in class etomica.virial.MayerGeneralSpherical
-
- setBox(IBox) - Method in class etomica.virial.MayerHardSphere
-
- setBox(IBox) - Method in class etomica.virial.MayerPTAtt
-
- setBox(IBox) - Method in class etomica.virial.MayerPUGeneral
-
- setBox(IBox) - Method in class etomica.virial.MayerSphericalPlus
-
- setBox(IBox) - Method in class etomica.virial.MayerSphericalPTAtt
-
- setBox(IBox) - Method in class etomica.virial.MayerSSSeries
-
- setBox(IBox) - Method in class etomica.virial.MayerWell
-
- setBox(IBox) - Method in class etomica.virial.MayerXSpherical
-
- setBox(IBox) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtom
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomQ
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterDiagram
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingScale
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- setBox(IBox) - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterSamplingWeight
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirial
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBD
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBDBin
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalField
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldRho
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialIC
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialSWWE
-
- setBox(IBox) - Method in class etomica.virial.MuFGeneral
-
- setBox(IBox) - Method in class etomica.virial.MuGeneral
-
- setBox(IBox) - Method in class etomica.virial.P1IntraLambda
-
- setBox(IBox) - Method in class etomica.virial.PotentialCommonAtomic
-
- setBox(IBox) - Method in class etomica.virial.PotentialEmulCached
-
- setBox(IBox) - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- setBox(IBox) - Method in class etomica.virial.PotentialGroup3PI
-
- setBox(IBox) - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- setBox(IBox) - Method in class etomica.virial.PotentialGroupPI
-
- setBox(IBox) - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- setBox(IBox) - Method in class etomica.virial.PotentialNonAdditive
-
- setBox(IBox) - Method in class etomica.yukawa.P2HC2Yukawa
-
- setBox(IBox) - Method in class etomica.zeolite.MSDCoordWriter
-
- setBoxCanvas(DisplayCanvas) - Method in class etomica.graphics.DisplayBox
-
- setBoxFactory(SimulationVirialOverlap2.BoxClusterFactory) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setBoxIndex(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- setBoxSize(IVector) - Method in interface etomica.api.IBoundary
-
Scales the boundary dimensions such that the boundary's would be
inscribed within a rectangle of the of the given size.
- setBoxSize(IBox, int[]) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
Resizes simulation box to preserve periodic boundary conditions after rotation of lattice.
- setBoxSize(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Scales each boundary edge so that its length equals the corresponding value
in the given vector.
- setBoxSize(IVector) - Method in class etomica.space.BoundaryRectangular
-
Sets the size and shape of the rectangular boundary.
- setBoxSize(IVector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- setBPRes(double[]) - Method in class etomica.normalmode.MeterSolidDACut
-
- setBXX(double) - Method in class etomica.models.rowley.P2RepRowley
-
- setC(double, double) - Method in class etomica.normalmode.MinimizeHCP
-
- setC(double) - Method in class etomica.potential.P2Exp6
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSum
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizable
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- setCapacity(int) - Method in class etomica.nbr.list.AtomNeighborLists
-
Sets the number of up and down lists maintained by this instance.
- setCapacity(int) - Method in class etomica.nbr.list.AtomPotentialList
-
- setCapacity(int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Sets the number of up and down lists maintained by this instance.
- setCapacity(int) - Method in class etomica.nbr.list.molecule.MoleculePotentialList
-
- setCellDensity(double) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- setCellDensity(double) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- setCellDensity(double) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- setCellRange(int) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Sets the cell range to the given value.
- setCellRange(int) - Method in class etomica.nbr.cell.NeighborCellManager
-
Sets the cell range to the given value.
- setCellRange(int) - Method in class etomica.nbr.cell.PotentialMasterCell
-
- setCellRange(int) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- setCellRange(int) - Method in class etomica.nbr.list.PotentialMasterList
-
- setCellRange(int) - Method in class etomica.nbr.PotentialMasterHybrid
-
- setCellRange(int) - Method in class etomica.nbr.site.PotentialMasterSite
-
- setCellSize(double, double) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setCellSizeX(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setCellSizeX(double) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setCellSizeZ(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setCellSizeZ(double) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setCenterOfRotation(Point3f) - Method in class g3dsys.control.G3DSys
-
Set the molecule space location around which rotation occurs
- setCH2element(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setCH3element(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setChainlength(int) - Method in class etomica.models.hexane.MCMoveCBMC
-
- setChainLength(int) - Method in class etomica.modules.colloid.ColloidSim
-
- setChainLength(int) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setChainLength(int) - Method in class etomica.modules.colloid.MeterEnd2End
-
- setChainLength(int) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setChainLength(int) - Method in class etomica.modules.rheology.SimulationRheology
-
- setChainLength(int) - Method in class etomica.modules.sam.Sam
-
- setChainPhi(int, double) - Method in class etomica.modules.sam.Sam
-
- setChainPsi(double) - Method in class etomica.modules.sam.Sam
-
- setChainTheta(double) - Method in class etomica.modules.sam.Sam
-
- setChangeableModes(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Set the wavevectors that can be changed by the move.
- setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setCharge1(double) - Method in class etomica.potential.P2Electrostatic
-
Sets the charge on the first type of atom.
- setCharge1(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
Sets the charge on the first type of atom.
- setCharge2(double) - Method in class etomica.potential.P2Electrostatic
-
Sets the charge on the second type of atom.
- setCharge2(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
Sets the charge on the second type of atom.
- setChildCount(int[]) - Method in class etomica.species.SpeciesSpheresHetero
-
Directly sets the number of child atoms of each type created by this
factory.
- setChildIndex(int) - Method in interface etomica.api.IAtomType
-
- setChildIndex(int) - Method in class etomica.atom.AtomTypeLeaf
-
- setChildTypes(IAtomType[]) - Method in class etomica.species.SpeciesSpheresCustom
-
Sets the factories that make the child atoms of this factory's atom.
- setChildTypes(IAtomType[]) - Method in class etomica.species.SpeciesSpheresHetero
-
Sets the factories that make the child atoms of this factory's atom.
- setClient(Object) - Method in class etomica.simulation.DataStreamHeader
-
- setCloseFileEachTime(boolean) - Method in class etomica.data.DataLogger
-
Close the file and open a new one at each time INTERVAL.
- setCloseWindow(JButton) - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
-
- setCloseWindow(JButton) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- setColix(short) - Method in class org.jmol.g3d.Graphics3D
-
sets current color from colix color index
- setColix(short) - Method in class org.jmol.util.GData
-
- setColix(short) - Method in class org.jmol.util.MeshSurface
-
- setColixBack(short) - Method in class org.jmol.util.MeshSurface
-
- setCollapseOnReset(boolean) - Method in class etomica.util.HistoryComplete
-
Sets a flag that determines if the history is collapsed (to 100 data
points) when reset is called.
- setCollision(double, IAtom, PotentialHard) - Method in class etomica.integrator.IntegratorHard.Agent
-
Sets parameters associated with next two-body collision of this atom with another atom.
- setCollisionDiameter(double) - Method in class etomica.potential.P2HardSphere
-
Accessor method for collision diameter
- setCollisionRadius(double) - Method in class etomica.modules.osmosis.MeterOsmoticPressure
-
Sets the collision radius used to calculate accessible "area"
assuming that the relevant hard "boundaries" form right-angles with
other hard boundaries.
- setCollisionRadius(double) - Method in class etomica.modules.osmosis.P1HardWall
-
Distance from the center of the sphere to the boundary at collision.
- setCollisionRadius(double) - Method in class etomica.potential.P1HardBoundary
-
Distance from the center of the sphere to the boundary at collision.
- setCollisionRadius(double) - Method in class etomica.potential.P1HardMovingBoundary
-
Distance from the center of the sphere to the boundary at collision.
- setColloidMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setColloidSigma(double) - Method in class etomica.modules.colloid.ColloidSim
-
- setColor(char) - Method in interface etomica.graph.model.Edge
-
- setColor(char) - Method in class etomica.graph.model.impl.EdgeImpl
-
- setColor(char) - Method in class etomica.graph.model.impl.NodeImpl
-
- setColor(char) - Method in interface etomica.graph.model.Node
-
- setColor(IAtomType, Color) - Method in class etomica.graphics.ColorSchemeByType
-
- setColor(IAtomType, int, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
Sets atoms of the given type and number of bonds to be the given color.
- setColor(String) - Method in class etomica.modules.clustergenerator.Plot
-
- setColor(short) - Method in class g3dsys.images.Axes
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Ball
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Box
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Ellipse
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Line
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Triangle
-
set the color of the figure
- setColor(int) - Method in class org.jmol.g3d.Graphics3D
-
- setColor(int) - Method in class org.jmol.util.GData
-
- setColorIn(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
Color for atoms that are in the plane.
- setColorOut(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
Color for atoms that are out of the plane.
- setColorScheme(ColorScheme) - Method in class etomica.graphics.DisplayBox
-
Mutator method for the color scheme used for this display
- setColumn(int, float, float, float) - Method in class org.jmol.util.Matrix3f
-
Sets the specified column of this matrix3d to the three values provided.
- setColumn(int, float[]) - Method in class org.jmol.util.Matrix4f
-
Sets the specified column of this matrix4f to the four values provided.
- setColumn4(int, float, float, float, float) - Method in class org.jmol.util.Matrix4f
-
Sets the specified column of this matrix4f to the four values provided.
- setColumnA(int, float[]) - Method in class org.jmol.util.Matrix3f
-
Sets the specified column of this matrix3d to the four values provided.
- setColumnHeader(DataTag[], String) - Method in class etomica.graphics.DisplayTable
-
- setColumnInfoFactories(DataDoubleArray.DataInfoDoubleArrayFactory[]) - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Sets the DataInfoFactories for the columns
- setColumnNames(String[]) - Method in class etomica.graphics.DeviceTableModelGeneric
-
- setColumnV(int, Vector3f) - Method in class org.jmol.util.Matrix3f
-
Sets the specified column of this matrix3d to the vector provided.
- setCombinationProbability(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
Sets the probability that two radicals will bond instead of becoming
unreactive.
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Set the wavevectors that are removed.
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setComparedWV(int) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setComponent(Object) - Method in class etomica.graphics.DeviceSlider
-
- setComponent(Object) - Method in class etomica.graphics.DeviceSpinner
-
- setComponent(PNCO2GCPM.Component) - Method in class etomica.models.co2.PNCO2GCPM
-
- setComponent(PNGCPM.Component) - Method in class etomica.models.co2.PNGCPM
-
- setComponent(P2WaterSzalewicz.Component) - Method in class etomica.models.water.P2WaterSzalewicz
-
- setComponent(int, int, double) - Method in interface etomica.space.Tensor
-
- setComponent(int, int, double) - Method in class etomica.space1d.Tensor1D
-
- setComponent(int, int, double) - Method in class etomica.space2d.Tensor2D
-
- setComponent(int, int, double) - Method in class etomica.space3d.Tensor3D
-
- setComponent(int, int, double) - Method in class etomica.spaceNd.TensorND
-
- setComponent(int) - Method in class etomica.util.numerical.CalcGradientDifferentiable
-
- setComponentValues(String[][]) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setConfigDLPOLY(WriteConfigurationDLPOLY) - Method in class etomica.potential.PotentialDLPOLY
-
- setConfigP2DLPOLY(WriteConfigurationP2DLPOLY) - Method in class etomica.potential.P2DLPOLY
-
- setConfiguration(Configuration) - Method in class etomica.action.SimulationRestart
-
- setConfiguration(Configuration) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setConfiguration(Configuration) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setConfiguration(Configuration) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setConfiguration(Configuration) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setConfName(String) - Method in class etomica.action.WriteConfiguration
-
Sets the configuration name.
- setConfName(String) - Method in class etomica.action.WriteConfigurationBinary
-
Sets the configuration name.
- setConfName(String) - Method in class etomica.action.WriteConfigurationDLPOLY
-
Sets the configuration name.
- setConfName(String) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Sets the configuration name.
- setConformation(IConformation) - Method in class etomica.chem.models.ModelChain
-
Sets the Conformation for the molecule.
- setConformation(int, ConformationChainZigZag) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setConformation(IConformation) - Method in class etomica.species.Species
-
- setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setConformationParameters(double, double) - Method in class etomica.virial.SpeciesAlkane
-
- setConstrainScriptOrigin(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets whether scripts should only be loaded from the same
location as the documents referencing them.
- setConstraint(IPotentialAtomic) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterDDP
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterDP
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterTargetTP
-
- setConstraintAngle(double) - Method in class etomica.models.nitrogen.MeterDirectInitPert
-
- setConstraintAngle(double) - Method in class etomica.models.nitrogen.PRotConstraint
-
- setConstraintMap(int[]) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- setConstraintMap(int[]) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- setConstructorObject(Integer) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setContainingCubeEdgeLength(double) - Method in class etomica.math.geometry.TruncatedOctahedron
-
Sets the size of the truncated octahedron in terms of the edge length of
a cube that would contain it.
- setController(IController) - Method in interface etomica.action.ControllerAction
-
- setController(IController) - Method in class etomica.action.ControllerActionAdapter
-
- setController(IController) - Method in class etomica.graphics.Device
-
- setController(Controller) - Method in class etomica.graphics.DeviceControllerButton
-
- setController(IController) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the temperature slider controller.
- setController(IController) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the temperature slider controller.
- setController(IController) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the n- Cell # slider controller.
- setController(IController) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the x- and y- Cell # slider controller.
- setController(IController) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the eigenvalue # slider controller.
- setController(IController) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the wavevector # slider controller.
- setConvertedWV(int) - Method in class etomica.models.oneDHardRods.MeterF
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
-
- setCoordinateDefinition(CoordinateDefinitionNitrogen) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.CalcJacobian
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterDDP
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterDP
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterNormalMode
-
Sets the object that defines the real-space generalized coordinates.
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterTargetTP
-
- setCoordinateDefinition(CoordinateDefinitionParacetamol) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- setCoordinateDefinitionParacetamol(CoordinateDefinitionParacetamol) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2DoubleWell
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2PenetrableSphere
-
Mutator method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2SquareWell
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2TriangleWell
-
- setCoreDiameterSquared(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
- setCountOfMoleculesStrings(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setCountOfSpeciesSLM(SpinnerListModel, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setCountOfSpeciesSLMListener(ChangeListener[]) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setCountSpecies(int, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setCoupling(double) - Method in class etomica.spin.P2Spin
-
- setCriterion(IPotentialMolecular, NeighborCriterionMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterList.
- setCriterion(IPotentialAtomic, NeighborCriterion) - Method in class etomica.nbr.list.PotentialMasterList
-
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterList.
- setCriterion(IPotentialAtomic, NeighborCriterion) - Method in class etomica.nbr.site.PotentialMasterSite
-
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterCell.
- setCriterion(IPotential, NeighborCriterion) - Method in class etomica.potential.PotentialArray
-
Sets the criterion associated with the given potential
- setCriterion(IPotentialMolecular, NeighborCriterionMolecular) - Method in class etomica.potential.PotentialArrayMolecular
-
Sets the criterion associated with the given potential
- setCSPotential(P2SquareWellSurface) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveBcc
-
Sets the length of all primitive vectors to the given value.
- setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveFcc
-
Sets the length of all primitive vectors to the given value.
- setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
Sets the length of all primitive vectors to the given value.
- setCursor(int, Object) - Method in interface org.jmol.api.ApiPlatform
-
- setCursor(int, Object) - Method in class org.jmol.awt.Platform
-
- setCutoff(double) - Method in class etomica.modules.droplet.AtomFilterLiquid
-
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffRatio(double) - Method in class etomica.potential.P2MoleculeTruncated
-
- setCutoffRatio(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- setCVector(IVectorMutable) - Method in class etomica.action.BoxInflateAnisotropic
-
- setCXX(double) - Method in class etomica.models.rowley.P2RepRowley
-
- setD(float) - Method in class g3dsys.images.Ball
-
set the molspace diameter of the figure, when applicable
- setD(float) - Method in class g3dsys.images.Bond
-
set the molspace diameter of the figure, when applicable
- setD(float) - Method in class g3dsys.images.Ellipse
-
set the molspace diameter of the figure, when applicable
- setD2dfac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother
-
sets weight given to minimizing discontinuities in the 2nd derivative
(at data points)
- setD2fac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother
-
sets weight given to minimizing the 2nd derivative
- setD3dfac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother
-
- setD3fac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother
-
sets weight given to minimizing the 3nd derivative
- setDampingParams(int, int, double, int, boolean) - Method in class etomica.potential.P2QChemInterpolated
-
The energy u.
- setData(double[], double[]) - Method in class etomica.util.FastFourierTransform
-
Saves the two passed arrays of doubles into this class, real and
imaginary in order to transform.
- setData(double[], boolean) - Method in class etomica.util.FastFourierTransform
-
For passing only all reals (true) or all imaginaries (false)
- setData(double[]) - Method in class etomica.util.FastFourierTransform
-
For passing only one set of data - assumes passing all reals
- setDataResetAction(SimulationDataAction) - Method in class etomica.action.SimulationRestart
-
- setDataSink(int, IDataSink) - Method in class etomica.data.DataDistributer
-
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- setDataSink(IDataSink) - Method in class etomica.data.DataFork
-
Sets the given DataSink as the only one connected to this DataFork.
- setDataSink(int, IDataSink) - Method in class etomica.data.DataGroupSplitter
-
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- setDataSink(IDataSink) - Method in class etomica.data.DataLogger
-
- setDataSink(IDataSink) - Method in interface etomica.data.DataPipe
-
Sets the DataSink that will receive data from this DataPipe.
- setDataSink(IDataSink) - Method in class etomica.data.DataProcessor
-
Sets the sink receiving the data.
- setDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
-
- setDataSink(int, IDataSink) - Method in class etomica.data.DataSplitter
-
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- setDataSinkFactory(DataSplitter.IDataSinkFactory) - Method in class etomica.data.DataSplitter
-
- setDataSinks(IDataSink[]) - Method in class etomica.data.DataFork
-
- setDataSinks(IDataSink[]) - Method in interface etomica.data.DataPipeForked
-
Sets the list of DataSinks that receive the Data entering this DataFork.
- setDataSinks(IDataSink[]) - Method in class etomica.data.DataProcessorForked
-
- setDataSource(DataSourcePositioned) - Method in class etomica.data.meter.MeterProfile
-
Accessor method for the meter that defines the profiled quantity.
- setDataSource(DataSourceMolecular) - Method in class etomica.data.meter.MeterProfileByAtoms
-
Accessor method for the meter that defines the profiled quantity.
- setDataSource(DataSourceMolecular) - Method in class etomica.data.meter.MeterProfileByVolume
-
Accessor method for the meter that defines the profiled quantity.
- setDataSourceA(DataSourceScalar) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDataSourceB(DataSourceScalar) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDataSourceMuRoot(DataSourceMuRoot) - Method in class etomica.normalmode.DataSourceAvgPressure2
-
- setDecimalMode() - Method in class etomica.util.ScientificFormat
-
- setDecimalSeparatorAlwaysShown(boolean) - Method in class etomica.util.ScientificFormat
-
- setDecimalSliderLabelTable(Hashtable) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMajorTickSpacing(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMaximum(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMinimum(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMinorTickSpacing(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderValue(double) - Method in class etomica.graphics.DecimalSlider
-
- setDefaultColor(Color) - Method in class etomica.graphics.ColorScheme
-
- setDefaultDaDef(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setDefaultFontFamily(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the defaultFontFamily value.
- setDefaultLabel(String) - Method in class etomica.graphics.DisplayTextBox
-
Sets label to the given value if it was not previously set.
- setDefaultRotation() - Method in class g3dsys.control.G3DSys
-
Rescales slab and depth after image shell mode is toggled
or the number of layers changed.
- setDeformation(double) - Method in class etomica.modules.droplet.ConfigurationDroplet
-
- setDegeneracy(int[]) - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Invokes setDegeneracy(degeneracy, degeneracy.length), thus using all elements of given array.
- setDegeneracy(int[], int) - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Sets parameter that describes number of duplicate elements in the
iterates.
- setDelayExponent(double) - Method in class etomica.graphics.DeviceDelaySlider
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizable
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- setDeltaTmax(int) - Method in class etomica.zeolite.MSDProcessor
-
Allows for a new value of deltaTmax.
- setDeltaX(double) - Method in class etomica.util.HistogramExpanding
-
- setDenominator(int) - Method in interface etomica.graph.model.Coefficient
-
- setDenominator(int) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- setDensity(double) - Method in class etomica.box.Box
-
- setDensityProfileDump(IEtomicaDataSource) - Method in class etomica.data.DataProcessorChemicalPotential
-
- setDepth(double) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Set depth percentage
- setDepth(double) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Set depth percentage
- setDepth(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setDepthPercent(float) - Method in class g3dsys.control.G3DSys
-
- setDescription(JTextArea) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setDescription(JTextArea) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setDestination(IVector) - Method in class etomica.action.MoleculeActionTranslateTo
-
- setDestinationType(DestinationType) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the destinationType attribute value.
- setDiagram(int) - Method in class etomica.virial.ClusterSumStickyEF
-
- setDiagramSampling(boolean) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setDiameter(String, double) - Method in class etomica.atom.DiameterHashByElement
-
- setDiameter(String, double) - Method in class etomica.atom.DiameterHashByElementType
-
- setDiameter(IAtomType, double) - Method in class etomica.atom.DiameterHashByType
-
- setDiameterHash(DiameterHash) - Method in class etomica.graphics.DisplayBox
-
Sets the DiameterHash used by this DisplayBox.
- setDielectric(double) - Method in class etomica.potential.P2ReactionFieldDipole
-
Sets the dielectric constant of the fluid surrounding the cavity.
- setDielectric(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Sets the dielectric constant of the fluid surrounding the cavity.
- setDiffusePercent(int) - Static method in class org.jmol.util.GData
-
df in I = df * (N dot L) + sf * (R dot V)^p
- setDim(Dimension) - Method in class etomica.units.UnitGraphics
-
- setDimension(Dimension) - Method in class etomica.data.DataInfoFactory
-
Sets the dimension
- setDimension(Dimension) - Method in interface etomica.data.IEtomicaDataInfoFactory
-
Sets the dimension
- setDimensions(int, int, int, int, int, int, double, double, double, double, double, double) - Method in class etomica.config.GrainBoundaryConfiguration
-
- setDimensions(IVector) - Method in class etomica.lattice.CellLattice
-
- setDimensions(Tensor) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Sets the boundary tensor to equal the given tensor.
- setDims(int[]) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setDimx(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- setDimy(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- setDipole(double) - Method in class etomica.potential.P2HSDipole
-
- setDipole(double) - Method in class etomica.potential.P2LJDipole
-
- setDipoleMomentSquare(double) - Method in class etomica.rotation.P2LJDipole
-
- setDipoleSource(DipoleSource) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- setDipoleSource(DipoleSource) - Method in class etomica.potential.P1ExternalField
-
- setDipoleSource(DipoleSource) - Method in class etomica.potential.P2ReactionFieldDipole
-
Sets the dipole source used by this object should use.
- setDipoleSource(DipoleSource) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Sets the dipole source used by this object should use.
- setDipoleSource(DipoleSource) - Method in class etomica.potential.PotentialCalculationPhiSum
-
- setDipoleStrength(double) - Method in class etomica.models.water.DipoleSourceWater
-
Sets the strength (magnitude) of the dipole.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.ApiIntragroup
-
Specifies the direction, which applies only if iterating pairs
with a target atom; otherwise, if all pairs from group are indicated,
direction is ignored.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
- setDirection(IteratorDirective.Direction) - Method in interface etomica.atom.iterator.AtomsetIteratorDirectable
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.IteratorDirective
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MoleculeIteratorAll
-
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MoleculeIteratorMolecule
-
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MpiInterspecies1A
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MpiIntraspecies1A
-
Specifies the direction, which applies only if iterating pairs
with a target atom; otherwise, if all pairs from group are indicated,
direction is ignored.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MpiMolecule
-
Specifies the direction from which partners of a target atoms
are taken to form iterates.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.TripletInnerSequential
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Sets the iterator to return only up-list neighbors or down-list neighbors.
- setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.cell.Api1ACell
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.site.Api1ASite
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- setDirection(IVector) - Method in interface etomica.space.IOrientation
-
Sets the orientation's direction to be the given direction.
- setDirection(IVector) - Method in class etomica.space2d.Orientation2D
-
Sets this orientation to point in the given direction.
- setDirection(IVector) - Method in class etomica.space3d.Orientation3D
-
Sets this orientation to point in the given direction.
- setDirection(IVector) - Method in class etomica.space3d.OrientationFull3D
-
Sets this orientation to point in the given direction.
- setDirection(IVectorMutable) - Method in class etomica.spin.P1MagneticField
-
- setDirections(IVector, IVector) - Method in interface etomica.space3d.IOrientationFull3D
-
Sets the orientation's primary and secondary direction to be the given
directions.
- setDirections(IVector, IVector) - Method in class etomica.space3d.OrientationFull3D
-
- setDisp(boolean) - Method in class etomica.potential.P2QChemInterpolated
-
- setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- setDistanceToOrigin(double) - Method in class etomica.math.geometry.Plane
-
Sets perpendicular distance from the plane to the origin.
- setDoAdjustOnTime(boolean) - Method in class etomica.overlap.IntegratorOverlap
-
If true, causes the integrator to optimize how much each system runs
based on the wall clock time needed to run steps in each system.
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfiguration
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationBinary
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationDLPOLY
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- setDoApplyPBC(boolean) - Method in class etomica.nbr.cell.NeighborCellManager
-
- setDoApplyPBC(boolean) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- setDoApplyPBC(boolean) - Method in class etomica.nbr.list.NeighborListManager
-
- setDoAveraging(boolean) - Method in class etomica.util.HistogramNotSoSimple
-
turns "averaging" on or off.
- setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoft
-
- setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoftBD
-
- setDoClear(boolean) - Method in class etomica.graphics.DisplayPlot
-
- setDoConfigButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the config (and velocity) buttons.
- setDoCov(boolean) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setDoDensityInput(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the RDF plot.
- setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoDouble(boolean) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setDoDrawLines(DataTag[], boolean) - Method in class etomica.graphics.DisplayPlot
-
Sets the data set corresponding to the given tags to be have the data
points connected with lines or not.
- setDoEnforceBounds(boolean) - Method in class etomica.data.DataSourceUniform
-
- setDoExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoExchange(boolean[]) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setDoExchange(boolean[]) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- setDoExchangeCondensing(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Turn on replacement of exchanged groups of nodes with a single node (of
a different color)
- setDoExchangeCondensing(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
Turn on replacement of exchanged groups of nodes with a single node (of
a different color)
- setDoExchangeF(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Turn on replacement of eBonds with bonds that represent a single fBond
between an exchange group and another molecule (or another exchange
group).
- setDoExchangeF(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
Turn on replacement of eBonds with bonds that represent a single fBond
between an exchange group and another molecule (or another exchange
group).
- setDoExcludeBogusConfigs(boolean) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setDoExcludeBogusConfigs(boolean) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setDoExcludeNonNeighbors(boolean) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
- setDoExcludeNonNeighbors(boolean) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
- setDoExcludeNonNeighbors(boolean) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
- setDoExp(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoFastButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- setDoHB(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Enable construction of diagrams from the Hellmann-Bich formulation
- setDoHB(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
Enable construction of diagrams from the Hellmann-Bich formulation
- setDoIncludeACInError(boolean) - Method in class etomica.data.AccumulatorAverage
-
Include correction to the uncertainty from block correlation function as
prescribed in
Kolafa, Jiri(1986) 'Autocorrelations and subseries averages in Monte
Carlo Simulations', Molecular Physics (59) 1035
- setDoIncludeCoefficients(boolean) - Method in class etomica.graph.viewer.GraphMap
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoLegend(boolean) - Method in class etomica.graphics.DisplayPlot
-
Mutator for flag determining if a legend is to be shown.
- setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Only include graphs with nonadditive bonds.
- setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoMultiFromPair(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoMultiFromPair(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoNegativeExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoNegativeExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoNMoleculeSlider(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the # of molecules slider.
- setDoNonEquilibrium(boolean) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- setDoPBC(boolean) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- setDoPBC(boolean) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- setDoRDF(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the RDF plot.
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- setDoResetFilter(boolean) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- setDoScaling(boolean) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setDoSecondDerivative(boolean) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- setDoShowCurrent(boolean) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setDoStrictBlockData(boolean) - Method in class etomica.data.AccumulatorAverageFixed
-
Sets the accumulator to base statistics only on block data (where that
makes sense).
- setDoWiggle(boolean) - Method in class etomica.virial.simulations.SimulationVirial
-
- setDoWiggle(boolean) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setDrawable(boolean) - Method in class g3dsys.images.Figure
-
- setDrawable(boolean) - Method in class g3dsys.images.ImageShell
-
- setDrawBoundary(int) - Method in class etomica.graphics.DisplayCanvas
-
- setDrawBoundaryType(int) - Method in class g3dsys.images.ImageShell
-
Sets the boundary drawing style
- setDrawingHeight(int) - Method in class etomica.graphics.DisplayBox
-
Set the height of the drawing area (only relevant for 1D)
- setDrawingThickness(int) - Method in class etomica.potential.P1HardBoundary
-
- setDrawNumbersOfBlack(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- setDrawNumbersOfWhite(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- setDrawOverflow(boolean) - Method in class etomica.graphics.DisplayBox
-
- setDrawPoints(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- setDsABase(double) - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- setDsABase(double) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDsBBase(double) - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- setDsBBase(double) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDst(File) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
When converting a single source, dst can be a file.
- setDSVO(DataSourceVirialOverlap) - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets the DataSource that retrieves data from both boxs and provides
information to the integrator about their progress.
- setDv(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- setEdgeLength(double) - Method in class etomica.math.geometry.Cube
-
- setEdgeLength(double) - Method in class etomica.math.geometry.Square
-
- setEdgeLength(double) - Method in class etomica.math.geometry.TruncatedOctahedron
-
Specifies the common length of all edges of the truncated octahedron.
- setEdgeLengths(IVector) - Method in class etomica.math.geometry.Cuboid
-
Sets the three edge lengths of the cuboid, taking
each element of the given vector for the length of
the corresponding cuboid edge.
- setEdgeLengths(double, double, double) - Method in class etomica.math.geometry.Cuboid
-
Sets the lengths of all edges of the cuboid.
- setEdgeLengths(IVector) - Method in class etomica.math.geometry.LineSegment
-
Sets the length equal to the element of the (presumably 1D) vector.
- setEdgeLengths(IVector) - Method in class etomica.math.geometry.Rectangle
-
Sets the two edge lengths of the rectangle, taking
each element of the given vector for the length of
the corresponding rectangle edge.
- setEdgeLengths(double, double) - Method in class etomica.math.geometry.Rectangle
-
- setEdgeLengths(IVector) - Method in interface etomica.math.geometry.Rectangular
-
Specifies the D edge lengths needed to describe the shape
of the polytope.
- setEdgeVector(int, IVector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- setEdgeVectors(IVector[]) - Method in class etomica.math.geometry.Parallelepiped
-
Sets the lengths and directions of all edges of the parellelepiped.
- setEdgeVectors(IVector[]) - Method in class etomica.math.geometry.Parallelogram
-
Sets the lengths and directions of all edges of the parellelepiped.
- setEdgeVectors(IVector[]) - Method in interface etomica.math.geometry.Parallelotope
-
Specifies the polytope via an array of edge vectors.
- setEditable(boolean) - Method in class etomica.graphics.DeviceBox
-
- setEditValues(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setEditValues(boolean) - Method in class etomica.graphics.DeviceThermoSlider
-
Set whether the temperature text box should be editable.
- setEditValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set whether the temperature text box should be editable.
- setEditValues(boolean) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set whether the x- and y-Cell # text box should be editable.
- setEditValues(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set whether the eigenvalue # text box should be editable.
- setEditValues(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set whether the wavevector # text box should be editable.
- setEditVariables(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setEditVariables(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
Informs the move of the eigenvectors for the selected wave vector.
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
Informs the move of the eigenvectors for the selected wave vector.
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Informs the move of the eigenvectors
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterF
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setEigenVectors(double[][][]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setEigenVectors(double[][][]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setEigenVectors(double[][]) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
Informs the move of the eigenvectors for the k=0 wave vector.
- setEigenVectors(double[][][]) - Method in class etomica.normalmode.MCMoveSingleMode
-
Informs the move of the eigenvectors for the selected wave vector.
- setEigenvectors(double[]) - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- setEigenvectors(double[][][]) - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- setEigenvectors(double[][][]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setElement(IElement) - Method in class etomica.chem.models.ModelChain
-
Sets the Element used for the leaf atoms in the chain.
- setElement(int, int, float) - Method in class org.jmol.util.Matrix3f
-
Sets the specified element of this matrix3d to the value provided.
- setElement(int, int, float) - Method in class org.jmol.util.Matrix4f
-
Sets the specified element of this matrix4f to the value provided.
- setEllipsoidMatrix(Vector3f[], float[], Vector3f, Matrix3f) - Static method in class org.jmol.util.Quadric
-
- setEnabled(boolean) - Method in interface etomica.api.IPotentialMaster
-
Permits enabling/disabling of all potentials.
- setEnabled(IPotentialMolecular, boolean) - Method in interface etomica.api.IPotentialMaster
-
Indicates that the specified potential should not contribute to potential
calculations.
- setEnabled(IPotentialAtomic, boolean) - Method in interface etomica.api.IPotentialMaster
-
Indicates that the specified potential should not contribute to potential
calculations.
- setEnabled(boolean) - Method in class etomica.graphics.DeviceNSelector
-
- setEnabled(boolean) - Method in class etomica.graphics.DeviceSlider
-
Sets the deivce's slider and textfield to be enabled or not.
- setEnabled(IPotentialAtomic, boolean) - Method in class etomica.potential.PotentialGroup
-
Indicates that the specified potential should not contribute to potential
calculations.
- setEnabled(boolean) - Method in class etomica.potential.PotentialMaster
-
- setEnabled(IPotentialMolecular, boolean) - Method in class etomica.potential.PotentialMaster
-
- setEnabled(IPotentialAtomic, boolean) - Method in class etomica.potential.PotentialMaster
-
- setEnabled(boolean) - Method in class etomica.potential.PotentialMasterLrc
-
- setEnabled(boolean) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- setEnabled(boolean) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- setEnablePBC(boolean) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- setEnd(Point3f) - Method in class g3dsys.images.Line
-
- setEnd(float, float, float) - Method in class g3dsys.images.Line
-
- setEnergyBase(double) - Method in class etomica.normalmode.BoltzmannProcessor
-
- setEnergyFac(double) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
sets the harmonic bond "energy" factor
The probability of the bond have length x is proportional to exp(-factor*x^2)
(there is no temperature involved here)
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
sets the harmonic bond "energy" factor
The probability of the bond to have length x is proportional to exp(-factor*x^2)
(there is no temperature involved here)
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingScale
-
- setEnergyMeter(MeterPotentialEnergy) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setEnergyMeter(MeterPotentialEnergy, MeterPotentialEnergy) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setEnergyMeter(MeterPotentialEnergy) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setEpsilon(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setEpsilon(double) - Method in class etomica.modules.adsorption.P1Wall
-
- setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.colloid.P1Wall
-
- setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- setEpsilon(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- setEpsilon(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
-
- setEpsilon(double) - Method in class etomica.modules.rosmosis.P1Tether
-
- setEpsilon(double) - Method in class etomica.modules.sam.P1WCAWall
-
- setEpsilon(double) - Method in class etomica.modules.vle.VLESim
-
- setEpsilon(double) - Method in class etomica.potential.P22CLJQ
-
- setEpsilon(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociation
-
Accessor method for depth of well.
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2LennardJones
-
Mutator method for Lennard-Jones energy parameter
- setEpsilon(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
Mutator method for Lennard-Jones energy parameter
- setEpsilon(double) - Method in class etomica.potential.P2LJDipole
-
- setEpsilon(double) - Method in class etomica.potential.P2LJQ
-
- setEpsilon(double) - Method in class etomica.potential.P2LJQQ
-
- setEpsilon(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setEpsilon(double) - Method in class etomica.potential.P2Morse
-
- setEpsilon(double) - Method in class etomica.potential.P2PenetrableSphere
-
Accessor method for height of core.
- setEpsilon(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Mutator method for depth of well.
- setEpsilon(double) - Method in class etomica.potential.P2SoftSphere
-
Mutator method for soft-sphere energy parameter
- setEpsilon(double) - Method in class etomica.potential.P2SquareWell
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2TriangleWell
-
- setEpsilon(double) - Method in class etomica.potential.P2WCA
-
Mutator method for the energy parameter
- setEpsilon(double) - Method in class etomica.potential.P3BondAngle
-
Sets the characteristic energy of the potential
- setEpsilon(double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
Sets the characteristic energy of the potential
- setEpsilon(double) - Method in class etomica.rotation.P2LJDipole
-
- setEpsilon(double) - Method in class etomica.units.systems.LJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setEpsilon(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
Mutator methods for size and energy parameters.
- setEpsilon6(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setEpsilonCG(double) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setEpsilonCore(double) - Method in class etomica.potential.P2DoubleWell
-
Accessor method for depth of well
- setEpsilonCore(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Sets height of penetrable core.
- setEpsilonNR(double) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setEpsilonWell(double) - Method in class etomica.potential.P2DoubleWell
-
- setEpsInner(double) - Method in class etomica.potential.P2PenetrableBond
-
- setEpsOuter(double) - Method in class etomica.potential.P2PenetrableBond
-
- setEquilibrating(boolean) - Method in class etomica.integrator.mcmove.MCMoveManager
-
- setErrMulti(double) - Method in class etomica.potential.P2HePCKLJS
-
- setEthanolParams(int) - Static method in class etomica.models.rowley.EthanolRouteParams
-
- setEValNum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the current value for the eigenvalue # slider/text box.
- setEValNum(int) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setEventInterval(int) - Method in class etomica.integrator.Integrator
-
Sets value of interval between successive firing of integrator interval events.
- setExcludeArticulationPair(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to exclude clusters having an articulation pair.
- setExcludeArticulationPoint(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to exclude clusters having an articulation point.
- setExcludeNodalPoint(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to exclude clusters having a nodal point.
- setExecuteOnload(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets whether or not scripts attached to the DOM using 'onload'
event attribute must be executed before rasterizing.
- setExp(int) - Method in class etomica.virial.MayerSSSeries
-
Sets the HS diameter.
- setExpGroupingSize(int) - Method in class etomica.util.ScientificFormat
-
- setExpMaximumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setExpMinimumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setExpNegativePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setExpNegativeSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setExponentialMode() - Method in class etomica.util.ScientificFormat
-
- setExpPositivePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setExpPositiveSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setExpPSpan(double) - Method in class etomica.normalmode.MeterDDP
-
- setExpPSpan(double) - Method in class etomica.normalmode.MeterDP
-
- setExternalField(IVector) - Method in class etomica.potential.P1ExternalField
-
- setExtraData(IEtomicaDataSource) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
Sets a data source used to draw an extra set of "atoms".
- setExtraTargetClusters(ClusterAbstract[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setFactory(SimulationRunner) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setFalseLabel(String) - Method in class etomica.action.ActionToggle
-
Specifies the button's label when the toggle is set to false.
- setFalseLabel(String) - Method in class etomica.graphics.DeviceToggleButton
-
Specifies the button's label when the toggle is set to false.
- setFalseLabel(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Specifies the button's label when the toggle is set to false.
- setFile(File) - Method in class etomica.action.PDBWriter
-
Sets the file to write to.
- setFile(File) - Method in class etomica.action.XYZWriter
-
Sets the file to write to.
- setFile(String) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
- setFile(String) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- setFileName(String) - Method in class etomica.action.PDBWriter
-
Sets the file name to write to.
- setFileName(String) - Method in class etomica.action.WriteConfiguration
-
- setFileName(String) - Method in class etomica.action.WriteConfigurationBinary
-
- setFileName(String) - Method in class etomica.action.XYZWriter
-
Sets the file name to write to.
- setFileName(String) - Method in class etomica.data.DataLogger
-
Define the name of the output file.
- setFileName(String) - Method in class etomica.dimer.IntegratorDimerMin
-
Set's the filename of the output of this integrator.
- setFileName(String) - Method in class etomica.dimer.IntegratorDimerRT
-
Set's the filename of the output of this integrator.
- setFilename(String) - Method in class etomica.models.oneDHardRods.WriteHistograms
-
- setFileName(String) - Method in class etomica.normalmode.NormalModesMolecular
-
- setFileName(String) - Method in class etomica.normalmode.NormalModesPotential
-
- setFilename(String) - Method in class etomica.normalmode.WriteS
-
- setFileWriter(FileWriter) - Method in class etomica.data.DataArrayWriter
-
- setFileWriter(FileWriter) - Method in interface etomica.data.DataLogger.DataWriter
-
Sets the FileWriter to be used for actual file I/O.
- setFileWriter(FileWriter) - Method in class etomica.data.DataTableWriter
-
- setFilter(AtomFilter) - Method in class etomica.modules.droplet.MeterDeformation
-
- setFitToWindow(boolean) - Method in class etomica.graphics.DisplayTable
-
If true, columns will be squeezed so table fits to window; if false,
table will exceed window size, and to view full width must be placed in a
scroll pane.
- setFixedCOM(boolean) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- setFixedDaDef(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- setFixedOrientation(boolean) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setFixedSpecies(ISpecies) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- setFixedWall(FixedWall) - Method in class etomica.interfacial.IntegratorFixedWall
-
- setFlexCancelOnly(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
This method only effects the graphs returned by getMSMCGraphs
- setFlexCancelOnly(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
This method only effects the graphs returned by getMSMCGraphs
- setFlexibleMode() - Method in class etomica.util.ScientificFormat
-
- setFluctuationFactor(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setFluidNbrDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setFont(JmolFont) - Method in class org.jmol.g3d.Graphics3D
-
- setFont(JmolFont) - Method in class org.jmol.util.GData
-
- setFontFid(byte) - Method in class org.jmol.g3d.Graphics3D
-
- setFontFid(byte) - Method in class org.jmol.util.GData
-
- setForce(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setForceconstant(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setForceconstant(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setForceSum(PotentialCalculationForceSum) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- setForceSum(PotentialCalculationForceSum) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setFrac(double) - Method in class etomica.normalmode.MCMoveHarmonicEin
-
Sets the fraction of the systems energy from the normal mode
contribution.
- setFrac(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
Sets the fraction that the system is coupled to measured energy.
- setFrac(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- setFrac(double) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setFrac(double) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setFrameProperties() - Method in class etomica.virial.GUI.containers.AppFrameMixtureBuilder
-
- setFreeRadicalColor(IAtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- setFrequency(MCMove, double) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Sets the trial frequency for the given move to the given frequency.
- setFugacityFraction(double[]) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Specifies the fugacity fractions for the set of species that can participate in
an exchange move.
- setFullBondColor(IAtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
-
- setFullColor(IAtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- setFunction(IFunction) - Method in class etomica.data.DataSourceFunction
-
- setFunction(FunctionInvertible) - Method in class etomica.modifier.ModifierFunctionWrapper
-
- setFunction(FunctionMultiDimensionalDifferentiable) - Method in class etomica.util.numerical.Function1d
-
- setG(double) - Method in class etomica.modules.droplet.P1Smash
-
- setG1(Graph) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- setG2(Graph) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- setGamma(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- setGamma(double) - Method in class etomica.potential.P3BondAngleDreiding
-
Sets the characteristic energy of the potential
- setGammaPositionAndOrientation(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setGBplane(int[]) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
Allows a user to specify a plane for GB
- setGlobal() - Method in class org.jmol.script.ScriptVariable
-
- setGlobalMoveInterval(double) - Method in class etomica.integrator.IntegratorManagerMC
-
Sets the average interval between box-swap trials.
- setGoal(int) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
-
controls greyscale rendering
- setGroupingSize(int) - Method in class etomica.util.ScientificFormat
-
- setGroupingUsed(boolean) - Method in class etomica.util.ScientificFormat
-
- setH(double) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- setH(double) - Method in class etomica.spin.P1MagneticField
-
- setH(double) - Method in class etomica.util.numerical.FiniteDifferenceDerivative
-
- setHardCoreDiamterSq(double) - Method in class etomica.potential.P22CLJQ
-
- setHardCoreDiamterSq(double) - Method in class etomica.potential.P2LJQ
-
- setHardCoreDiamterSq(double) - Method in class etomica.rotation.P2LJDipole
-
- setHarmonicFudge(double) - Method in interface etomica.normalmode.NormalModes
-
Set the fudge factor applied to frequencies.
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes1DHR
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes2D
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes3D
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesFromFile
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesMolecular
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesPotential
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setHarmonicFudge(double) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setHarmonicPressure(double[], double) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- setHarmonicWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setHarmonicWV(int) - Method in class etomica.normalmode.MCMoveSingleMode
-
The harmonic wavevector and all wavevectors with higher numbers are not
able to be changed by this MCMove.
- setHashMapAtomsetIterator(HashMap<String[], AtomsetIteratorBasisDependent>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapAtomTypeLikePairs(HashMap<String[], IAtomType[]>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapAtomTypesUnlikePairs(HashMap<String[], IAtomType[]>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setHashMapPotentialIntraBonded(HashMap<String[], IPotential>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setHashMapPotentialNonBonded(HashMap<String[], IPotential>) - Method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
-
- setHeight(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
In less than or equal to zero, the height is not
constrained on the output image.
- setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterElongation
-
- setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterStrain
-
- setHexagonal(boolean) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- setHistogram(Histogram) - Method in class etomica.data.AccumulatorHistogram
-
- setHistogram(Histogram) - Method in class etomica.models.oneDHardRods.WriteHistograms
-
- setHistogramming(boolean) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setHistory(History) - Method in class etomica.data.AccumulatorHistory
-
- setHistoryLength(int) - Method in interface etomica.util.History
-
Sets the number of data points to be tracked by the History.
- setHistoryLength(int) - Method in class etomica.util.HistoryCollapsing
-
Sets the number of values kept in the history.
- setHistoryLength(int) - Method in class etomica.util.HistoryComplete
-
Sets the number of values kept in the history.
- setHistoryLength(int) - Method in class etomica.util.HistoryScrolling
-
Sets the number of values kept in the history.
- setHOptimizer(boolean) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- setId(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- setID(int) - Method in class g3dsys.images.Figure
-
Set the ID of the figure.
- setIdentity() - Method in class org.jmol.util.Matrix3f
-
Sets this Matrix3f to identity.
- setIdentity() - Method in class org.jmol.util.Matrix4f
-
Sets this Matrix4f to identity.
- setIgnoredAtomType(IAtomType) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- setIgnoreOverlap(boolean) - Method in class etomica.action.IntegratorReset
-
- setIgnoreOverlap(boolean) - Method in class etomica.action.SimulationRestart
-
- setIgnoreOverlap(boolean) - Method in class etomica.zeolite.ZeoliteSimStart
-
- setIgnoreReferenceAvg(boolean) - Method in class etomica.virial.overlap.DataVirialOverlap
-
Directs this class to ignore the reference average when deciding how
much time to spend on each system.
- setImage(Image) - Method in class etomica.util.Grabber.ImagePanel
-
- setImageShells(int) - Method in class etomica.graphics.DisplayBox
-
Changes the value of image shells, and increases/decreases scale accordingly.
- setImax(int) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setImportantAtoms() - Method in class etomica.action.IntegratorDimerApproach
-
- setIncludeAdiabatic(boolean) - Method in class etomica.graphics.DeviceThermoSelector
-
- setIncludeHeader(boolean) - Method in class etomica.data.DataArrayWriter
-
Directs the writer to include column headers or not
- setIncludeHeader(boolean) - Method in class etomica.data.DataTableWriter
-
Directs the writer to include column headers or not
- setIncludeLrc(boolean) - Method in class etomica.atom.iterator.IteratorDirective
-
Sets flag indicating if lrc potentials (long-range correction) should be
included.
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterHyperVirial
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPotentialEnergy
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressure
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressureMolecular
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressureTensor
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.liquidLJ.MeterPU
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.modules.vle.MeterPressure2
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.normalmode.MeterPressureSuperBox
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setIndex(int) - Method in interface etomica.api.IAtom
-
Informs the IAtom of its index, which is used to construct the address.
- setIndex(int) - Method in interface etomica.api.IAtomType
-
Informs the ISpecies what its index should be.
- setIndex(int) - Method in interface etomica.api.IBox
-
Informs the IBox what its index is.
- setIndex(int) - Method in interface etomica.api.IMolecule
-
Informs the IMolecule of its index.
- setIndex(int) - Method in interface etomica.api.ISpecies
-
Informs the ISpecies what its index should be.
- setIndex(int) - Method in class etomica.atom.Atom
-
- setIndex(int) - Method in class etomica.atom.AtomTypeLeaf
-
- setIndex(int) - Method in class etomica.atom.Molecule
-
- setIndex(int) - Method in class etomica.box.Box
-
- setIndex(int) - Method in class etomica.species.Species
-
- setIndexed(int) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Tells the PNG encoder to reduce the image to 256 colors, so the
PNG file is indexed.
- setIndexSelectedSpecies(int) - Method in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
-
- setInflateDimensions(boolean[]) - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
For anisotropic volume change, indicates dimension in which volume is perturbed.
- setInflater(BoxInflate) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setInitialStateConditions(double, double) - Method in class etomica.kmc.IntegratorKMC
-
- setInitialStateConditions(double, double) - Method in class etomica.kmc.IntegratorKMCCluster
-
- setInitVolume(IVector) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- setInitVolume(IVector) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- setInnerIterator(GraphIterator) - Method in class etomica.graph.iterators.CartesianIterator
-
- setInnerList(IAtomList) - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setInnerList(IMoleculeList) - Method in class etomica.atom.iterator.MpiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setInnerPermutator(DefaultPermutator) - Method in class etomica.graph.iterators.CartesianPermutator
-
- setInnerWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- setInnerWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
- setInputData(double[], double[]) - Method in class etomica.util.numerical.AkimaSpline
-
- setInputData(double[], double[], double[]) - Method in class etomica.util.numerical.AkimaSplineSmoother
-
- setInputData(double[], double[], double[]) - Method in class etomica.util.numerical.AkimaSplineSmootherDy
-
- setInputData(double[], double[], double[], double[]) - Method in class etomica.util.numerical.AkimaSplineSmootherDy
-
Set the nominal values for x and y and uncertainty in y (ey).
- setInputFileName(String) - Method in class etomica.util.ReadParameters
-
Sets the fileName to read the parameters from.
- setInputFileName(String) - Method in class etomica.util.WriteParameters
-
Sets the fileName to read the parameters from.
- setInt(int) - Method in class org.jmol.util.Rgb16
-
- setInteger(boolean) - Method in class etomica.graphics.DeviceBox
-
Sets a flag indicating if the value should be displayed as an integer.
- setIntegerDisplay(boolean) - Method in class etomica.graphics.DisplayTextBox
-
- setIntegrationParameters(double, double, double, double, int, int) - Method in class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- setIntegrator(IIntegrator) - Method in interface etomica.action.IntegratorAction
-
- setIntegrator(IIntegrator) - Method in class etomica.action.IntegratorActionAdapter
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.DataProcessorChemicalPotential
-
- setIntegrator(IntegratorHard) - Method in class etomica.data.DataSourceCountCollisions
-
- setIntegrator(IIntegrator) - Method in class etomica.data.DataSourceCountSteps
-
- setIntegrator(IntegratorMD) - Method in class etomica.data.DataSourceCountTime
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
Sets the integrator.
- setIntegrator(IntegratorHard) - Method in class etomica.data.DataSourceTensorVirialHard
-
Informs meter of the integrator for its box, and zeros elapsed-time counter
- setIntegrator(IntegratorMD) - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressure
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorHard) - Method in class etomica.data.meter.MeterPressureHard
-
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
- setIntegrator(IntegratorHard) - Method in class etomica.data.meter.MeterPressureHardTensor
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressureMolecular
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorVelocityVerlet) - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets the integrator associated with this class.
- setIntegrator(IntegratorBox) - Method in class etomica.graphics.DeviceThermoSelector
-
- setIntegrator(IntegratorBox) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Sets the integrator associated with this class.
- setIntegrator(IntegratorVelocityVerlet) - Method in class etomica.meam.DataProcessorCvMD
-
- setIntegrator(IntegratorHard) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
- setIntegrator(IntegratorHard) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- setIntegrator(IntegratorHard) - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
- setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterViscosity
-
- setIntegrator(IntegratorBox) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setIntegrator(IntegratorHarmonic) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Sets the integrator for the device.
- setIntegrator(IntegratorHarmonic) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Sets the integrator for the device.
- setIntegrator(IntegratorBox) - Method in class etomica.normalmode.MeterPressureSuperBox
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorBox) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
Sets an integrator to use a source for the temperature to compute the
kinetic portion of the pressure.
- setIntegrator(IIntegrator) - Method in class etomica.zeolite.MSDCoordWriter
-
- setIntegratorMC(IntegratorMC, int) - Method in class etomica.integrator.IntegratorMD
-
- setIntegratorOverlap(IntegratorOverlap) - Method in class etomica.normalmode.SimOverlapModule
-
- setIntegrators(IntegratorMC, IntegratorMD, IRandom) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setIntegrators(IntegratorBox, IntegratorBox) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Sets the integrator for the device.
- setInteractionRange(double) - Method in class etomica.nbr.CriterionPositionWall
-
Informs the criterion of the interaction range of the wall potential.
- setInteractionRange(double) - Method in class etomica.nbr.CriterionSimple
-
- setInteractionRange(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setIntercepts(double, double, double) - Method in class etomica.math.geometry.Plane
-
Reorients and positions the plane so that its intercepts with the
x-, y-, and z-axes are the given values, respectively.
- setInteriorColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- setInterval(long) - Method in class etomica.data.DataPumpListener
-
- setInterval(int) - Method in class etomica.listener.IntegratorListenerAction
-
- setInterval(int) - Method in class etomica.listener.IntegratorListenerGroupSeries
-
- setIntraMolecular(boolean) - Method in class etomica.nbr.CriterionMolecular
-
Configures to accept intra- (if argument is true) or inter-
(if argument is false) molecular pairs.
- setIntraMolecularCriterion(NeighborCriterion) - Method in class etomica.nbr.CriterionInterMolecular
-
Configures to use the given criterion for intramolecular pairs.
- setInverseNormixes() - Static method in class org.jmol.util.Normix
-
- setIs256() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- setIs864() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- setIsAlpha() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsAlpha() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setIsAppend(boolean) - Method in class etomica.action.XYZWriter
-
- setIsBeta() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsBetaHCP() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsBetaLatticeSum() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsDoLatticeSum() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheres
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresCustom
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresHetero
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresMono
-
- setIsFluctuationFromAvg(boolean) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setIsGamma() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsGamma() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setIsInteracting(boolean, int) - Method in class etomica.nbr.list.AtomPotentialList
-
Sets whether the atom is interacting or not with the potential
corresponding to the given index.
- setIsInteracting(boolean, int) - Method in class etomica.nbr.list.molecule.MoleculePotentialList
-
Sets whether the molecule is interacting or not with the potential
corresponding to the given index.
- setIsothermal() - Method in class etomica.graphics.DeviceThermoSlider
-
Set the Isothermal button to its selected state.
- setIsothermal(boolean) - Method in class etomica.integrator.IntegratorBox
-
- setIsothermal(boolean) - Method in class etomica.integrator.IntegratorMD
-
- setIsothermal(boolean) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setIsothermal(boolean) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the Isothermal button to its selected state.
- setIsothermalButtonsVisibility(boolean) - Method in class etomica.graphics.DeviceThermoSlider
-
- setIsothermalButtonsVisibility(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- setIsUpperBound(boolean) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- setIterator(AtomIterator) - Method in class etomica.data.DataSourceRmsVelocity
-
Sets the iterator defining the atoms for which the RMS velocity is
calculated.
- setIterator(AtomsetIteratorBoxDependent) - Method in class etomica.data.meter.MeterBondOrderParameterQ
-
Sets the iterator that gives the atoms over which the order parameter
will be calculated.
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterKineticEnergy
-
Sets the iterator that defines the atoms which are summed for
their total kinetic energy.
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterLocalDensity
-
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterMeanSquareDisplacement
-
- setIterator(MoleculeIteratorAllMolecules) - Method in class etomica.data.meter.MeterRadiusGyration
-
Mutator method for the iterator that generates the atom pairs used to
tabulate the ROG.
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.zeolite.MSDCoordWriter
-
- setJmax(int) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setJSpinnerCountOfSpecies1(JSpinner, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setK(IVector) - Method in class etomica.lattice.LatticeSum
-
- setK(IVector) - Method in class etomica.lattice.LatticeSumCrystal
-
- setK(IVector) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- setK(IVectorMutable) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- setKappa(double) - Method in class etomica.yukawa.P2Yukawa
-
Mutator methods for size and energy parameters.
- setKinetic(DataSourceScalar) - Method in class etomica.data.meter.MeterEnergy
-
- setKineticEnergyMeter(DataSourceScalar) - Method in class etomica.data.meter.MeterTemperature
-
- setL(int) - Method in class etomica.data.meter.MeterBondOrderParameterQ
-
Sets the value of the parameter l, to indicate if Q4 or Q6 is to be computed.
- setLabel(String) - Method in class etomica.data.DataInfoFactory
-
Sets the label
- setLabel(String) - Method in interface etomica.data.IEtomicaDataInfoFactory
-
Sets the label
- setLabel(String) - Method in class etomica.graphics.DeviceBox
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DeviceButton
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DeviceButtonGroup
-
Sets the label for the group of radio buttons
- setLabel(String) - Method in class etomica.graphics.DeviceSelector
-
- setLabel(String) - Method in class etomica.graphics.DeviceSlider
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DeviceSpinner
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.Display
-
Accessor method of the label describing the display.
- setLabel(String) - Method in class etomica.graphics.DisplayTextBox
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setLabel(String) - Method in class etomica.modifier.ModifierGeneral
-
- setLabel(String) - Method in class etomica.zeolite.DeviceButtonSingle
-
Sets the value of a descriptive label using the given string.
- setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DeviceBox
-
- setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DisplayTextBox
-
- setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setLabels(String[]) - Method in class etomica.graphics.DeviceTernarySelector
-
Labels used to indicate the three component fractions.
- setLabelType(DeviceBox.LabelType) - Method in class etomica.graphics.DeviceBox
-
Sets the label type to "border" or "string".
- setLabelType(DisplayTextBox.LabelType) - Method in class etomica.graphics.DisplayTextBox
-
- setLabelType(DisplayTextBox.LabelType) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setLambda(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setLambda(double) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setLambda(double) - Method in class etomica.potential.P2DoubleWell
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2SquareWell
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2TriangleWell
-
- setLanguage(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the user language.
- setLattice(FiniteLattice) - Method in class etomica.graphics.ColorSchemeCell
-
- setLattice(FiniteLattice) - Method in class etomica.lattice.CellLattice.NeighborIterator
-
- setLattice(SpaceLattice) - Method in class etomica.lattice.LatticeSum
-
- setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLattice.Iterator
-
- setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Sets the lattice from which the iterates are given.
- setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
- setLattice(FiniteLattice) - Method in interface etomica.lattice.SiteIterator
-
Sets the lattice having the sites to be given by this iterator.
- setLattice(CellLattice) - Method in class etomica.nbr.cell.ApiAACell
-
- setLattice(CellLattice) - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- setLatticeBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setLatticeBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setLatticeConstant(double) - Method in interface etomica.lattice.CubicLattice
-
Sets the size of the unit cell, the length of each edge.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicBcc
-
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicDiamond
-
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicFcc
-
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicSimple
-
The lattice constant is the size of the cubic primitive vectors.
- setLatticeCorrec(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDADB
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDirectSamplingTarget
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterTargetTP
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
-
- setLayers(int) - Method in class g3dsys.images.ImageShell
-
Sets the number of image shell layers to use
- setLeafIndex(int) - Method in interface etomica.api.IAtom
-
Sets the atom's global index to the give value.
- setLeafIndex(int) - Method in class etomica.atom.Atom
-
- setLegend(DataTag[], String) - Method in class etomica.graphics.DisplayPlot
-
- setLength(double) - Method in class etomica.math.geometry.LineSegment
-
Sets the length of the segment to the given value, keeping
its orientation and the position of its midpoint fixed.
- setLength(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setLength(double) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- setLength(int) - Method in class org.jmol.util.StringXBuilder
-
- setLengthAlkaneChain(int, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setLinPSpan(double) - Method in class etomica.normalmode.MeterDDP
-
- setLinPSpan(double) - Method in class etomica.normalmode.MeterDP
-
- setLiquidColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- setLiquidFilter(AtomFilter) - Method in class etomica.modules.droplet.P2Cohesion
-
- setList(IAtomList) - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Sets the list that will be used to generate the pairs.
- setList(IAtomList) - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Sets the list for iteration.
- setList(IMoleculeList) - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
-
Sets the list for iteration.
- setList(IMoleculeList) - Method in class etomica.atom.iterator.MpiIntraArrayList
-
Sets the list that will be used to generate the pairs.
- setLnBias(int, double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setLnBias(int, double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setLocale(Locale) - Static method in class etomica.graph.view.rasterizer.Messages
-
Implements Localizable.setLocale(Locale).
- setLocalVisitor(TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
-
Replaces the current logger implementation by a new one.
- setLogLevel(int) - Static method in class org.jmol.util.Logger
-
Activates all logging levels up through a given level.
- setLongWall(int, boolean, boolean) - Method in class etomica.potential.P1HardBoundary
-
- setLowerTorsLimit(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setM(Matrix3f) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this axis-angle to the rotational component of the passed
matrix.
- setM(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the double value of the Matrix3f argument.
- setM(Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a copy of the passed matrix m1.
- setM(Matrix3f) - Method in class org.jmol.util.Quaternion
-
- setM3(Matrix3f) - Method in class org.jmol.util.Matrix4f
-
Sets the rotational component (upper 3x3) of this matrix to the matrix
values in the single precision Matrix3f argument; the other elements of
this matrix are initialized as if this were an identity matrix (ie, affine
matrix with no translational component).
- setMacrostateManager(MacrostateManager) - Method in class etomica.tmmc.IntegratorTMMC
-
- setMakeLrc(boolean) - Method in class etomica.potential.P2SoftSphericalTruncated
-
- setMakeReeHover(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to generate Ree-Hoover diagrams.
- setMass(double) - Method in class etomica.chem.elements.ElementSimple
-
Sets mass of this element and updates reciprocal mass accordingly.
- setMass(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setMass(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
Sets the mass; we assume the reduced mass is m/2 (correct for particles
with identical mass).
- setMass(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
Sets the mass; we assume the reduced mass is m/2 (correct for particles
with identical mass).
- setMass(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- setMass(double) - Method in class etomica.units.systems.LJ
-
- setMax(int) - Method in class etomica.lattice.IndexIteratorIncreasing
-
Sets a new maximum for iteration.
- setMaxBlocks(int) - Method in class etomica.data.AccumulatorAverageCollapsing
-
- setMaxBonds(int) - Method in class etomica.association.AssociationHelperBranched
-
- setMaxBonds(int) - Method in class etomica.association.AssociationHelperMolecule
-
- setmaxCosPhi(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setmaxCosPhi(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setmaxCosTheta(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setmaxCosTheta(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setMaxDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setMaxDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- setMaxElement(int) - Method in class etomica.lattice.IndexIteratorTriangular
-
Sets the largest allow value for any element to have.
- setMaxElement(int) - Method in class etomica.lattice.LatticeSum
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxElementMin(int) - Method in class etomica.lattice.IndexIteratorTriangular
-
- setMaxHeight(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
If less than or equal to zero, the maximum height
does not have any effect on the output image.
- setMaximum(double) - Method in class etomica.graphics.DeviceSlider
-
Sets maximum value of slider; should be called after
any calls to setPrecision.
- setMaximum(double) - Method in class etomica.graphics.DeviceSpinner
-
Sets maximum value of slider
- setMaximum(double) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the maximum value for the temperature.
- setMaximum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the maximum value for the temperature.
- setMaximum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the maximum value for the N-Cell #.
- setMaximum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the maximum value for the x- and y-Cell #.
- setMaximum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the maximum value for the eigenvalue #.
- setMaximum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the maximum value for the wavevector #.
- setMaximumFractionDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMaximumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMaximumSeparation(double) - Method in class etomica.potential.P2Fene
-
Accessor method for harmonic energy parameter
- setMaxIndex(int) - Method in class etomica.veos.HardRods
-
- setMaxIndex(int) - Method in class etomica.veos.VanderWaals
-
- setMaxInsertDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setMaxInsertDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- setMaxIterations(int) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setMaxIterations(int) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- setMaxIterations(int) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setMaxIterations(int) - Method in class etomica.modules.interfacial.FitTanh
-
- setMaxIterations(int) - Method in class etomica.surfacetension.FitTanh
-
- setMaxLatticeShell(int) - Method in class etomica.lattice.LatticeSumCrystal
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxLatticeShell(int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxLatticeShell(int) - Method in class etomica.normalmode.HarmonicCrystal
-
- setMaxLatticeShell(int) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- setMaxLatticeShell(int) - Method in class etomica.normalmode.NormalModesPotential
-
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setMaxLength(int) - Method in class etomica.association.MCMoveAtomMonomer
-
- setMaxLength(int) - Method in class etomica.association.MCMoveAtomSmer
-
- setMaxLength(int) - Method in class etomica.association.MCMoveBiasUB
-
- setMaxLength(int) - Method in class etomica.association.MCMoveRotateAssociated
-
- setMaxNbrsVapor(int) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- setMaxPhi(double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- setMaxPhi(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- setMaxSample(double) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
- setMaxSleep(int) - Method in class etomica.graphics.DeviceDelaySlider
-
- setMaxSteps(long) - Method in class etomica.action.ActionIntegrate
-
Mutator method for the number of doStep steps to be
performed by this integrator after it is started.
- setMaxSteps(long) - Method in class etomica.action.activity.ActivityIntegrate
-
Mutator method for the number of doStep steps to be
performed by this integrator after it is started.
- setMaxWidth(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
If less than or equal to zero, the maximum width
does not have any effect on the output image.
- setMaxWidth(int) - Method in class etomica.util.ScientificFormat
-
the the maximum width of the decimal format.
- setMCMove(MCMoveStepDependent) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- setMCMoveClusterTorsionMulti(MCMoveClusterTorsionMulti[]) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setMCMoveInsertDelete(MyMCMove, MyMCMove) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setMCMoves(MCMove[]) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Sets moves in given array to be integrator's set of moves, deleting any
existing moves.
- setMDStepRepetitions(int) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setMDStepRepetitions(int) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setMediaType(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the mediaType value.
- setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setMembraneThickness(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setMembraneThicknessPerLayer(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setMeter(DataSourceScalar) - Method in class etomica.graphics.DisplayScrollingGraph
-
Specifies the meter that generates the displayed value.
- setMeter(MeterNormalMode) - Method in class etomica.normalmode.WriteS
-
- setMeter(IEtomicaDataSource) - Method in class etomica.virial.simulations.SimulationVirial
-
- setMeter(MeterVirial, int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setMeter(MeterVirial, int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setMeter(int, MeterVirial) - Method in class etomica.virial.simulations.SimulationVirialPT
-
- setMeterPotentialEnergy(DataSourceScalar) - Method in class etomica.integrator.IntegratorBox
-
- setMeterTemperature(MeterTemperature) - Method in class etomica.integrator.IntegratorMD
-
Sets the temperature meter used to calculate temperature for
velocity rescaling.
- setMethanolParams(int) - Static method in class etomica.models.rowley.MethanolRouteParams
-
- setMillerIndex(int, int) - Method in class etomica.lattice.LatticePlane
-
Sets the i-th Miller index to h, keeping the others fixed.
- setMillerIndices(int[]) - Method in class etomica.lattice.LatticePlane
-
Sets the plane to the orientation specified by the given Miller indices
applied to the current primitive.
- setMinBondedAtomDistance(double) - Method in class etomica.association.AssociationHelperBranched
-
- setMinBondedAtomDistance(double) - Method in class etomica.association.AssociationHelperDouble
-
- setMinBondedMoleculeDistance(double) - Method in class etomica.association.AssociationHelperMolecule
-
- setMinDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- setMinimum(double) - Method in class etomica.graphics.DeviceSlider
-
Sets minimum value of slider; should be called after
any calls to setPrecision.
- setMinimum(double) - Method in class etomica.graphics.DeviceSpinner
-
Sets minimum value of spinner
- setMinimum(double) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the minimum value for the temperature.
- setMinimum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the minimum value for the temperature.
- setMinimum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the minimum value for the N-Cell #.
- setMinimum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the minimum value for the x- and y-Cell #.
- setMinimum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the minimum value for the eigenvalue #.
- setMinimum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the minimum value for the wavevector #.
- setMinimumFractionDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMinimumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMinMax(int, int) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setMinMu(double) - Method in class etomica.normalmode.DataSourceMuRoot1
-
- setMinRadicalSites(int) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- setMobileSpecies(ISpecies) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- setModelSelectedSpecies(ModelSelectedSpecies) - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- setModelSpeciesSelection(ModelSpeciesSelection) - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- setModeNum(int[]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setModes(int[]) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
Sets the indices of the harmonic modes of the k=0 wave vector which
should be sampled.
- setModifier(ModifierBoolean) - Method in class etomica.action.ActionToggle
-
Specifies the boolean modifier that is set between true and false by the
action.
- setModifier(Modifier) - Method in class etomica.graphics.DeviceBox
-
Specifies the modifier that receives the edit.
- setModifier(ModifierBoolean) - Method in class etomica.graphics.DeviceCheckBox
-
Returns the boolean modifier set by this button.
- setModifier(Modifier) - Method in class etomica.graphics.DeviceNSelector
-
- setModifier(Modifier) - Method in class etomica.graphics.DeviceSlider
-
- setModifier(Modifier) - Method in class etomica.graphics.DeviceSpinner
-
- setModifier(Modifier) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the temperature modifier object.
- setModifier(ModifierBoolean, String, String) - Method in class etomica.graphics.DeviceToggleButton
-
- setModifier(ModifierBoolean) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Returns the boolean modifier set by this button.
- setModifier(Modifier) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the temperature modifier object.
- setModifier(Modifier) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the eigenvalue # modifier object.
- setModifier(Modifier) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the wavevector # modifier object.
- setMolecule(IMolecule, IMolecule) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- setMolecule(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorArrayList
-
Sets the first atom for iteration.
- setMolecule(IMolecule) - Method in interface etomica.atom.iterator.MoleculeIteratorMoleculeDependent
-
- setMolecule(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorSinglet
-
Defines atom returned by iterator and leaves iterator unset.
- setMolecule(int, int) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
-
- setMolecule(int, int) - Method in interface etomica.paracetamol.LatticeEnergyParacetamol
-
- setMolecule(int, int) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
-
- setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.potential.PotentialCalculationTorqueSum
-
- setMoleculeInfo(ISpecies, P2SemiclassicalMolecular.MoleculeInfo) - Method in class etomica.potential.P2SemiclassicalMolecular
-
- setMoleculeListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeListDisplayString(ArrayList<String>) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setMoleculeListDisplayTable(JTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayTable(JTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeLists(IMoleculeList[]) - Method in class etomica.box.AtomSetAllMolecules
-
- setMoleculeOffset(IVectorMutable) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setMoleculeOffset(IVectorMutable) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setMoleculePosition(IAtomPositionDefinition) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setMolecules() - Method in class etomica.action.IntegratorDimerApproach
-
- setMoleculeSource(MoleculeSource) - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- setMoleculeSource(MoleculeSource) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
Sets the AtomSource this class uses to pick molecules to delete.
- setMoleculeSource(MoleculeSource) - Method in class etomica.models.hexane.MCMoveCBMC
-
Sets the AtomSource used to select molecules acted on by MC trials.
- setMoleculeSource(MoleculeSource) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- setMoleculeSource(MoleculeSource) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- setMoment(double) - Method in class etomica.modules.vle.VLESim
-
- setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setMomentOfInertia(double) - Method in class etomica.atom.AtomTypeOrientedSphere
-
- setMomentOfInertia(IVector) - Method in class etomica.species.SpeciesSpheresRotatingMolecule
-
Sets the species' moment of inertia to the given moment.
- setMomentSquare(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setMonomerColor(Color) - Method in class etomica.association.ColorSchemeSmer
-
Sets the color used for all dimers.
- setMonomerMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setMovable(boolean) - Method in class etomica.graphics.DisplayCanvas
-
- setMovable(boolean) - Method in class etomica.graphics.DisplayPolytope
-
- setMovableAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerLJadatom
-
- setMovableAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMadatom
-
- setMovableAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCLJadatom
-
- setMovableAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCMEAMadatom
-
- setMovableAtomsCube(IVectorMutable, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMGB
-
- setMovableAtomsList() - Method in class etomica.dimer.SimDimerMEAMGB
-
- setMovableAtomsSphere(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMGB
-
- setMove(MCMove) - Method in class etomica.data.DataSourceAcceptanceRatio
-
Sets the move for which the acceptance ratio is reported.
- setMoveManager(MCMoveManager) - Method in class etomica.integrator.IntegratorManagerMC
-
- setMoveManager(MCMoveManager) - Method in class etomica.integrator.IntegratorMC
-
- setMu(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
Sets a nominal bias for states that have not yet been visited.
- setMu(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Mutator method for the chemical potential of the insertion/deletion species.
- setMu(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setMu(double, double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setMu(double) - Method in class etomica.normalmode.DataSourceAvgPressure
-
- setMu(double) - Method in class etomica.normalmode.DataSourceFEHistogram
-
- setMu(double) - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- setMu(double) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- setMu(double) - Method in class etomica.normalmode.DataSourcePMu
-
- setMV(Matrix3f, Vector3f) - Method in class org.jmol.util.Matrix4f
-
Initializes a Matrix4f from the rotation matrix
and translation.
- setN(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- setN(int) - Method in class etomica.potential.P4TorsionDreiding
-
- setN(int) - Method in class etomica.veos.Ushcats
-
- setName(String) - Method in class etomica.data.meter.MeterDihedralAngle
-
- setName(String) - Method in class etomica.data.meter.MeterMomentumCOM
-
- setName(String) - Method in class etomica.data.meter.MeterPositionCOM
-
- setName(String) - Method in class etomica.data.meter.MeterPressureHardTensor
-
- setName(String) - Method in class etomica.data.meter.MeterRDF
-
- setName(String) - Method in class etomica.data.meter.MeterRDFPC
-
- setName(String) - Method in class etomica.data.meter.MeterTensorVelocity
-
- setName(String) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- setName(String) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setName(String) - Method in class etomica.normalmode.MeterNormalMode
-
- setName(String) - Method in class org.jmol.script.ScriptVariable
-
- setNBins(int) - Method in class etomica.data.AccumulatorHistogram
-
Sets the number of bins in each histogram.
- setNBins(int) - Method in interface etomica.util.Histogram
-
Sets the number of bins used by the Histogram.
- setNBins(int) - Method in class etomica.util.HistogramDiscrete
-
- setNBins(int) - Method in class etomica.util.HistogramExpanding
-
Sets the number of bins to n.
- setNBins(int) - Method in class etomica.util.HistogramNotSoSimple
-
- setNBins(int) - Method in class etomica.util.HistogramReweightedData
-
- setNBins(int) - Method in class etomica.util.HistogramSimple
-
- setNbrDistance(double) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- setNCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the n-Cell # modifier object.
- setNCellNum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the current value for the N-Cell # slider/text box.
- setNCellNum(int) - Method in class etomica.normalmode.NormalModes3D
-
- setNCells(int[]) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- setNCells(int[]) - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- setNCellsX(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNCellsX(int) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setNCellsZ(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNCellsZ(int) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setNCrossLinkersAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNDiAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNDiol(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNegativePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setNegativeSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setNeighborDistance(double) - Method in class etomica.lattice.CellLattice.NeighborIterator
-
Defines neighbors to be all cells that are within the given distance
from a central cell.
- setNeighborRange(double) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the neighbor range of the criterion.
- setNeighborRange(double) - Method in class etomica.nbr.CriterionSimple
-
- setNeighborRange(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setNewWindowParametersForExport() - Method in class org.jmol.util.GData
-
- setNextCriterion(IteratorDirective.PotentialCriterion) - Method in class etomica.atom.iterator.IteratorDirective.PotentialCriterion
-
- setNGraft(int) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setNInsert(int) - Method in class etomica.data.meter.MeterWidomInsertion
-
Number of Widom insertions attempted with each call to currentValue
- setNInsert(int) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Number of Widom insertions attempted with each call to currentValue
- setNInsert(int) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Number of Widom insertions attempted with each call to currentValue
- setNMajor(int) - Method in class etomica.graphics.DeviceSlider
-
- setNMaxReweight(int) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setNMinor(int) - Method in class etomica.graphics.DeviceSlider
-
- setNMolecules(ISpecies, int) - Method in interface etomica.api.IBox
-
Sets the number of molecules in this box of the given ISpecies to n.
- setNMolecules(ISpecies, int) - Method in class etomica.box.Box
-
- setNMonoAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNMonoOl(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNo72B2B3NonAdd(boolean) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- setNoisyAdjustment(boolean) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to
assign a noisy shade to the surface it will render
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.util.GData
-
- setNominalFluctuation(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setNominalReference(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setNominalTheta(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- setNominalTheta(double) - Method in class etomica.normalmode.MeterThetaDeviation
-
- setNoOfSpheres(JTextField) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- setNoOfSteps(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setNoOfSteps(int) - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- setNormalModes(NormalModes) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setNormalModes(NormalModes) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setNormalPoint(IVector, IVector) - Method in class etomica.math.geometry.Plane
-
Defines the plane via a normal vector (1st argument) and
a point (2nd argument).
- setNormalVector(IVector) - Method in class etomica.math.geometry.Plane
-
Sets the orientation of the plane to be normal to the given vector.
- setNPoints(int) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setnPoints(int[]) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setnReactCO(int) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- setNRows(int) - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Sets the number of rows.
- setNSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the post slider value changed action.
- setNSpheres(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setNSpheres(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setNthSpeciesAdded(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setNthSpeciesSelectedIndex(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setNTicks(int) - Method in class etomica.graphics.DisplayScrollingGraph
-
- setNullPotential(PotentialHard) - Method in class etomica.integrator.IntegratorHard.Agent
-
- setNullPotential(PotentialHard, IAtomType) - Method in class etomica.integrator.IntegratorHard
-
Sets the "null" potential for the given AtomType.
- setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setNumAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setNumAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setNumAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- setNumAlpha(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- setNumAlpha(int) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setNumAlpha(int) - Method in class etomica.normalmode.MeterTargetTP
-
- setNumAlpha(int) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- setNumAlpha(int) - Method in class etomica.overlap.MeterOverlap
-
- setNumAlpha(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- setNumAlpha(int) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- setNumAlpha(int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
Sets the number of alpha values used for the production stage of the
simulation
- setNumAlpha(int) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Sets the number of alpha values used for the production stage of the
simulation.
- setNumAtoms(int) - Method in class etomica.chem.models.ModelChain
-
Sets the number of atoms per chain molecule.
- setNumBeads(int) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setNumber(double) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- setNumberFraction(double[]) - Method in class etomica.species.SpeciesSpheresHetero
-
Sets the number fraction of each child atom type made by
this factory.
- setNumberOfModesChanged(int) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setNumberOfTrials(int) - Method in class etomica.models.hexane.MCMoveCBMC
-
- setNumBoxes(int) - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
Specifies the number of boxes that are tracked.
- setNumCells(int) - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
-
- setNumCO(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNumCollapseBins(int) - Method in class etomica.util.HistoryCollapsing
-
Sets the number of "collapse" bins.
- setNumDigitColumns(int) - Method in class etomica.graphics.DisplayTable
-
- setNumEquilibrationSubsteps(int) - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Sets the number of steps equilibration steps performed at each
thermodynamic state point before data collection begins.
- setNumerator(int) - Method in interface etomica.graph.model.Coefficient
-
- setNumerator(int) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- setNumFactors(int) - Method in interface etomica.graph.model.Graph
-
- setNumFactors(int) - Method in class etomica.graph.model.impl.GraphImpl
-
- setNumGraft(int) - Method in class etomica.modules.colloid.ColloidSim
-
- setNumLeafAtoms(int) - Method in class etomica.species.SpeciesSpheres
-
Specifies the number of child atoms in each atom constructed by this factory.
- setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setNumO2(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNumP(int) - Method in class etomica.normalmode.MeterDDP
-
- setNumP(int) - Method in class etomica.normalmode.MeterDP
-
- setNumRawDataDoubles(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Sets the number of times the random block generation method is used.
- setNumSubSteps(long) - Method in class etomica.overlap.IntegratorOverlap
-
Sets the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
- setNumSubsteps(int) - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Sets the number of steps performed at each thermodynamic state point.
- setNumSubSteps(int) - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
- setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setNumThreads(int, IBox) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
-
- setNumThreads(int, IBox) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
-
- setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
Sets the number of configurational bias trials
- setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
Sets the number of configurational bias trials
- setNumXCells(int) - Method in class etomica.modules.sam.Sam
-
- setNumZCells(int) - Method in class etomica.modules.sam.Sam
-
- setNValues(int) - Method in class etomica.data.DataSourceUniform
-
Sets the number of uniformly spaced values.
- setOelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setOffset(IVector) - Method in class etomica.config.ConformationChainLinear
-
- setOffset(IVector) - Method in class etomica.config.ConformationLinear
-
- setOffset(IVectorMutable) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setOmegaSquared(double[][], double[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setOmegaSquared(double[][], double[]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setOmegaSquared(double[][]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setOmegaSquared(double[][], double[]) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setOmegaSquared(double[][]) - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- setOmegaSquared(double[][]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setOneEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the "eigenvalues" button to its selected state.
- setOneEVal(boolean) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setOneEValButtonsVisibility(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- setOneWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the "wave vector" button to its selected state.
- setOneWV(boolean) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setOneWVButtonsVisibility(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- setOnlyConnected(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to only generate clusters that are singly-connected.
- setOnlyDoublyConnected(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to only generate clusters that are doubly-connected.
- setOrderBeta(int) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setOrientation(IMolecule, IOrientationFull3D) - Method in interface etomica.atom.OrientationCalc
-
Sets the orientation of the given molecule to be equal to the given
orientation.
- setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.atom.OrientationCalcAtom
-
- setOrientation(IMolecule, double[]) - Method in interface etomica.atom.OrientationCalcQuaternion
-
- setOrientation(IVector) - Method in class etomica.config.ConformationChainLinear
-
- setOrientation(IVector) - Method in class etomica.config.ConformationLinear
-
- setOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater3P
-
- setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater3P
-
- setOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater4P
-
- setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater4P
-
- setOrientation(IOrientationFull3D) - Method in class etomica.space3d.RotationTensor3D
-
- setOrientationCalc(ISpecies, OrientationCalc) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setOrientationCalc(ISpecies, OrientationCalc) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- setOrientationCalc(ISpecies, OrientationCalcQuaternion) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- setOrientations(IVector[][], double[], CoordinateDefinitionHSDimer.IntegerFunction) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setOrientationSites(IAtomTypeOriented, DisplayBoxCanvasG3DSys.OrientedSite[]) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- setOrientationVectorAlpha(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorAlpha(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setOrientationVectorBeta(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorBetaInitial(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorBetaLatticeSum(ISpace, double, double[][]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorGamma(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorGamma(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setOrigin(IVector) - Method in class etomica.lattice.LatticePlane
-
Sets the origin from which the position of the atom is measured.
- setOriginShift(int, int) - Method in class etomica.graphics.DisplayBox
-
Amount (in pixels) of a simple shift (translation) applied in determing origin.
- setOrtho(boolean, boolean) - Method in class etomica.dimer.IntegratorDimerRT
-
Set's the Dimer search's orthogonality criteria.
- setOtherAngles(double[]) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setOtherDensities(double[]) - Method in class etomica.normalmode.MeterDDP
-
- setOtherDensities(double[]) - Method in class etomica.normalmode.MeterDP
-
- setOtherSwitchFrac(double[]) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setOtherTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setOtherTemperatures(double[]) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setOtherTemperatures(double[]) - Method in class etomica.normalmode.MeterTargetTP
-
- setOut(PrintStream) - Method in class etomica.data.DataSinkConsole
-
Sets the output print stream where data is written.
- setOuterGraph(Graph) - Method in class etomica.graph.iterators.CartesianIterator
-
- setOuterIterator(GraphIterator) - Method in class etomica.graph.iterators.CartesianIterator
-
- setOuterList(IAtomList) - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setOuterList(IMoleculeList) - Method in class etomica.atom.iterator.MpiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setOuterPermutation(byte[]) - Method in class etomica.graph.iterators.CartesianPermutator
-
- setOuterPermutator(DefaultPermutator) - Method in class etomica.graph.iterators.CartesianPermutator
-
- setOverlapSplitter(DataSplitter) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- setOverwrite(boolean) - Method in class etomica.normalmode.WriteS
-
- setPaddingSigma(double) - Method in class etomica.graphics.DisplayBox
-
Sets the amount of padding added around the edge of the drawing area.
- setPaintInterval(IBox, int) - Method in class etomica.graphics.SimulationGraphic
-
setPaintInterval()
Sets the integrator interval between repaint actions to the value
specified for the given Box.
- setParameter(String, String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setParameterLimits(String, double, double) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the minimum and maximum allowable values for a function parameter.
- setParameters(IAtomType, ParameterSetMEAM) - Method in class etomica.meam.PotentialMEAM
-
- setParameters(String) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- setParameters(double) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setParameters(String) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setParameters(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
Parameter calculation method.
- setParametersIMC(IAtomType, ParameterSetMEAM) - Method in class etomica.meam.PotentialMEAM
-
- setParameterWrapper(ParameterBase) - Method in class etomica.util.ParseArgs
-
Sets the parameterWrapper
- setParameterWrapper(ParameterBase) - Method in class etomica.util.ReadParameters
-
Sets the parameterWrapper
- setParameterWrapper(ParameterBase) - Method in class etomica.util.WriteParameters
-
Sets the parameterWrapper
- setParams() - Method in class etomica.virial.BnJHBVArgon_Analytic
-
- setParent(IMolecule) - Method in interface etomica.api.IAtom
-
Informs the Atom that the given AtomGroup is its parent.
- setParent(IMolecule) - Method in class etomica.atom.Atom
-
Informs the Atom that the given AtomGroup is its parent.
- setParseIntegerOnly(boolean) - Method in class etomica.util.ScientificFormat
-
- setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setPass2(boolean) - Method in class org.jmol.util.GData
-
- setPauseAfterEachAction(boolean) - Method in class etomica.action.activity.ActivityGroupSeries
-
- setPbcEnforcer(BoxImposePbc) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- setPbcEnforcer(BoxImposePbc) - Method in class etomica.nbr.list.NeighborListManager
-
- setPCenter(double[]) - Method in class etomica.normalmode.MeterDDP
-
- setPCenter(double[]) - Method in class etomica.normalmode.MeterDP
-
- setPcom(double[]) - Method in class etomica.util.numerical.Function1d
-
- setPeriodicity(boolean[]) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
- setPerpendicularTo(IVector) - Method in class etomica.space3d.Vector3D
-
- setPerspectiveDepth(boolean) - Method in class g3dsys.control.G3DSys
-
- setPHarmonic(double, double) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- setPhi(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setPhi(double) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- setPhi(double) - Method in class etomica.potential.P4TorsionDreiding
-
- setPhongExponent(int) - Static method in class org.jmol.util.GData
-
p in I = df * (N dot L) + sf * (R dot V)^p
- setPistonPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.BoundaryPistonCylinder
-
- setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayBox
-
Sets unit for conversion between simulation units and display pixels.
- setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayCanvas
-
Sets unit for conversion between simulation units and display pixels.
- setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayPolytope
-
Sets unit for conversion between simulation units and display pixels.
- setPixelUnitToMillimeter(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the millimeters per pixel constant.
- setPlaneColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the color of the plane.
- setPlayDumb(boolean) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
With "play dumb" on, the bias will simply try to produce a flat
histogram based on previously-measured free energy differences
(no fitting or defect free energy will be used).
- setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
-
- setPolytope(Polytope) - Method in class etomica.graphics.DisplayPolytope
-
Specifies the polytope for this display.
- setPolytopeCanvas(DisplayCanvas) - Method in class etomica.graphics.DisplayPolytope
-
- setPoreCenters(IVectorMutable[]) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setPoreDim(int) - Method in class etomica.space.BoundaryRectangularPore
-
Sets the periodic dimension to that indicated by the given value
(0 is x-dimension, 1 is y-dimension, etc.).
- setPoreRadius(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setPosition(IAtom, String) - Method in class etomica.config.ConfigurationFile
-
- setPosition(IAtom, String) - Method in class etomica.config.ConfigurationOrientedFile
-
- setPosition(double) - Method in class etomica.lattice.LatticePlane
-
Sets to the position of the i-th plane from the one through the origin.
- setPosition(IVector) - Method in class etomica.math.geometry.Hypersphere
-
- setPosition(IVector) - Method in class etomica.math.geometry.Polytope
-
Sets the position of the geometric center of the polytope.
- setPosition(IVector) - Method in interface etomica.math.geometry.Shape
-
Sets the position of the shape, which typically represents some central
point within it.
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.action.BoxImposePbc
-
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.atom.AtomFilterInShape
-
Sets position definition.
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.data.meter.MeterProfileByVolume
-
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.virial.CoordinatePairMoleculeSet
-
- setPositionSource(RandomPositionSource) - Method in class etomica.data.meter.MeterProfile
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Sets a new RandomPositionSource for this move to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
Sets a new RandomPositionSource for this move to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- setPositivePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setPositiveSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setPostAction(IAction) - Method in class etomica.graphics.Device
-
Sets an action to be performed after the primary action executed
by the device.
- setPotential(DataSourceScalar) - Method in class etomica.data.meter.MeterEnergy
-
- setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- setPotential(String) - Method in class etomica.modules.insertion.InsertionGraphic
-
- setPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- setPotential(String) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- setPotential(String) - Method in class etomica.modules.swmd.SwmdGraphic
-
- setPotential(IPotentialAtomic[]) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setPotential(IPotentialAtomic) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setPotential(Potential2) - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
- setPotential(IPotentialMolecular) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- setPotential(Potential2SoftSpherical) - Method in class etomica.normalmode.NormalModesPotential
-
- setPotential(Potential2SoftSpherical) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setPotential(PotentialGroup) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- setPotentialCalculation(PotentialCalculationEnergySum) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setPotentialCollectionFactory(ICollectionPotential) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setPotentialGroupInterNonBondedLike(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setPotentialGroupInterNonBondedUnlike(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setPotentialGroupIntraBonded(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setPotentialIntraBondedTorsion(IPotentialAtomic) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setPotentialJList(JList) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialJList(JList) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialList(Class[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialListAtoms() - Method in class etomica.dimer.SimDimerMEAMadatom
-
- setPotentialListAtoms() - Method in class etomica.kmc.SimKMCMEAMadatom
-
- setPotentialListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.data.meter.MeterHyperVirial
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.data.meter.MeterPressure
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPU
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCut
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.modules.vle.MeterPressure2
-
Sets the integrator associated with this instance.
- setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.BoxAgentSourceCellManagerList
-
- setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
-
- setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.NeighborCellManagerList
-
- setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.nbr.PotentialGroupHybrid
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setPotentialMaster(PotentialMasterList, IAtomType[]) - Method in class etomica.potential.P2SquareWellRobust
-
Informs the square-well class what the potential master is (if neighbor
listing is used) and the types of atoms interacting with this potential.
- setPotentialMaster(IPotentialMaster) - Method in class etomica.potential.PotentialGroup
-
- setPotentialMaster(IPotentialMaster) - Method in class etomica.virial.ClusterSumExternalField
-
- setPotentialMasterDADv2(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCut
-
- setPotentialMasterDADv2(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setPotentialMasterDADv2(IPotentialMaster, double[]) - Method in class etomica.normalmode.MeterSolidDACut
-
- setPotentialMC(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setPotentialMolecularNonBondedLike(IPotentialMolecular) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- setPotentialMolecularUnlike(IPotentialMolecular) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- setPotentialParamAndValuesString(String[][]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialParamDispayTable(JTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDispayTable(JTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamDisplayTM(ModelPotParamDisplayTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDisplayTM(ModelPotParamDisplayTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamString(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialPseudo(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setPotentialRange(double) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Sets the potential range to the given value.
- setPotentialRange(double) - Method in class etomica.nbr.cell.NeighborCellManager
-
Sets the potential range to the given value.
- setPotentialsClassList(Class[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialsCollectionBuilder(BuilderCollectionPotential) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setPotentialSites(String[]) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setPotentialsSelectedIndex(int[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialsSelectedIndex(int, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPreAction(IAction) - Method in class etomica.graphics.Device
-
Sets an action to be performed before the primary action executed
by the device.
- setPrecision(int) - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
- setPrecision(int) - Method in class etomica.graphics.DecimalSlider
-
Mutator method for precision of slider.
- setPrecision(int) - Method in class etomica.graphics.DeviceBox
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- setPrecision(int) - Method in class etomica.graphics.DeviceSlider
-
- setPrecision(int) - Method in class etomica.graphics.DeviceTernarySelector
-
Mutatator method for the precision of the mole fractions.
- setPrecision(int) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the precision of the scrollbar.
- setPrecision(int) - Method in class etomica.graphics.DisplayTable
-
Accessor method of the precision, which specifies the number of
significant figures to be displayed.
- setPrecision(int) - Method in class etomica.graphics.DisplayTextBox
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- setPrecision(int) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- setPrecision(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the precision of the scrollbar.
- setPrecision(int) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- setPrecisionLimit(int) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- setPrefactor(double) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setPreferredSize(int, int) - Method in class etomica.graphics.DeviceTable
-
Set the preferred size attribute of the scrolled window the table
sits on.
- setPrefix(Prefix) - Method in class etomica.units.PrefixedUnit
-
Changes prefix to given instance if prefixAllowed flag is true
- setPRes(double) - Method in class etomica.normalmode.MeterSolidDA
-
- setPressure(double) - Method in class etomica.association.MCMoveVolumeAssociated
-
- setPressure(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- setPressure(double) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setPressure(double) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setPressure(double, double, IFunction) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setPressure(double) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setPressure(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setPressure(double) - Method in class etomica.modules.adsorption.DataSourceDensityFunction
-
- setPressure(double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setPressure(double) - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- setPressure(double) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- setPressure(double) - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- setPressure(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setPrevX(float) - Method in class etomica.graphics.DisplayCanvas
-
- setPrevY(float) - Method in class etomica.graphics.DisplayCanvas
-
- setPrimitive(Primitive) - Method in class etomica.lattice.BravaisLattice
-
Sets the primitive for this lattice to the one given, and
updates the site positions.
- setPrimitive(Primitive) - Method in class etomica.lattice.LatticePlane
-
- setPrimitive(Primitive) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setProfileDim(int) - Method in class etomica.data.meter.MeterProfile
-
Accessor method for vector describing the direction along which the profile is measured.
- setProfileDim(int) - Method in class etomica.data.meter.MeterProfileByAtoms
-
Accessor method for vector describing the direction along which the profile is measured.
- setProfileDim(int) - Method in class etomica.data.meter.MeterProfileByVolume
-
Accessor method for vector describing the direction along which the profile is measured.
- setProfileDim(int) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- setProperty(String, String) - Method in interface etomica.graph.engine.Environment
-
- setProperty(String, String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- setProperty(String) - Method in class etomica.graphics.DeviceSlider
-
- setProperty(String) - Method in class etomica.graphics.DeviceSpinner
-
- SetPropertyFilter - Class in etomica.graph.operations
-
- SetPropertyFilter(Property) - Constructor for class etomica.graph.operations.SetPropertyFilter
-
- setPT2(boolean) - Static method in class etomica.potential.P2O2Bartolomei
-
- setPullFactor(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setPushInterval(long) - Method in class etomica.data.DataAccumulator
-
Accumulated data are pushed to the data sinks after every pushInterval calls
to putData.
- setQ(double) - Method in class etomica.chem.electrostatics.Charge
-
- setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P22CLJQ
-
- setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P2LJQ
-
- setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P2LJQQ
-
- setQuality(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the JPEG encoding quality.
- setQuaternions(double[]) - Method in class etomica.space3d.RotationTensor3D
-
- setQuiet(boolean) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Sets the quiet flag, indicating if unsafe-neighbor conditions should generate
an error message (would not want this if atoms were inserted in a MC
move, for example).
- setQuiet(boolean) - Method in class etomica.nbr.list.NeighborListManager
-
Sets the quiet flag, indicating if unsafe-neighbor conditions should generate
an error message (would not want this if atoms were inserted in a MC
move, for example).
- setQuiet(boolean) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setQuiet(boolean) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setQuiet(boolean) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setR0(double) - Method in class etomica.potential.P2Harmonic
-
Sets the the separation at which potential is at its minimum.
- setR2Cut(double) - Method in class etomica.data.meter.MeterBondOrderParameterQ
-
- setr2d2udr2(double[]) - Method in class etomica.virial.PercusYevick1QC
-
- setRadicalColor(IAtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
-
- setRadioGroupPostAction(IAction) - Method in class etomica.graphics.DeviceThermoSlider
-
Sets an action to be performed after a isothermal/adiabatic button is
pressed and the integrator's isothermality has been set.
- setRadius(double) - Method in class etomica.math.geometry.Hypersphere
-
- setRadius(double) - Method in class etomica.potential.P1SoftBoundary
-
Sets the radius.
- setRandom(IRandom) - Method in class etomica.simulation.Simulation
-
Set the simulation's random number generator to the given one.
- setRandom(IRandom) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setRandomCube(IRandom) - Method in interface etomica.space.IVectorRandom
-
Assigns each component to (its own) random value between -0.5 and + 0.5.
- setRandomCube(IRandom) - Method in class etomica.space1d.Vector1D
-
- setRandomCube(IRandom) - Method in class etomica.space2d.Vector2D
-
- setRandomCube(IRandom) - Method in class etomica.space3d.Vector3D
-
- setRandomCube(IRandom) - Method in class etomica.spaceNd.VectorND
-
- setRandomInSphere(IRandom) - Method in interface etomica.space.IVectorRandom
-
Assigns this vector to equal a point chosen randomly in the volume
of a unit spheres.
- setRandomInSphere(IRandom) - Method in class etomica.space1d.Vector1D
-
- setRandomInSphere(IRandom) - Method in class etomica.space2d.Vector2D
-
- setRandomInSphere(IRandom) - Method in class etomica.space3d.Vector3D
-
- setRandomInSphere(IRandom) - Method in class etomica.spaceNd.VectorND
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.association.AtomSourceRandomDimer
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.association.AtomSourceRandomSmer
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.association.MoleculeSourceRandomDimer
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.atom.AtomSourceRandomLeaf
-
Sets the random number generator used to pick atoms
- setRandomNumberGenerator(IRandom) - Method in class etomica.atom.AtomSourceRandomSpecies
-
Sets the random number generator used to pick atoms
- setRandomNumberGenerator(IRandom) - Method in class etomica.atom.MoleculeSourceRandomMolecule
-
Sets the random number generator used to pick molecules
- setRandomSphere(IRandom) - Method in interface etomica.space.IVectorRandom
-
Assigns this vector to equal a point chosen randomly on the
surface of a unit sphere.
- setRandomSphere(IRandom) - Method in class etomica.space1d.Vector1D
-
- setRandomSphere(IRandom) - Method in class etomica.space2d.Vector2D
-
- setRandomSphere(IRandom) - Method in class etomica.space3d.Vector3D
-
Creating a random unit vector on unit sphere Uses only two random number
generator at a time
Based on M.P.
- setRandomSphere(IRandom) - Method in class etomica.spaceNd.VectorND
-
Creating a random unit vector on unit sphere Uses only two random number
generator at a time
Based on M.P.
- setRange(int[]) - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
Sets the range used to define the neighboring sites.
- setRange(double, double) - Method in class etomica.meam.PotentialCuLREP
-
- setRange(double) - Method in class etomica.meam.PotentialEFS
-
- setRange(double) - Method in class etomica.meam.PotentialFeEAM
-
- setRange(double) - Method in class etomica.meam.PotentialFeEAM_LS
-
- setRange(double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- setRange(int, double, double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- setRange(double, double) - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- setRange(double) - Method in class etomica.modules.adsorption.P1Wall
-
- setRange(double) - Method in class etomica.modules.colloid.P1Wall
-
- setRange(double) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- setRange(double) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- setRange(double) - Method in class etomica.nbr.cell.PotentialMasterCell
-
- setRange(double) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Sets the interaction range, which affects the cell-list neighbor iteration
used to generate candidate neighbors for neighbor listing.
- setRange(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- setRange(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Sets the range that determines how far to look for neighbors.
- setRange(double) - Method in class etomica.nbr.list.NeighborListManager
-
Sets the interaction range, which affects the cell-list neighbor iteration
used to generate candidate neighbors for neighbor listing.
- setRange(double) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- setRange(double) - Method in class etomica.nbr.list.PotentialMasterList
-
Sets the range that determines how far to look for neighbors.
- setRange(double) - Method in class etomica.nbr.PotentialMasterHybrid
-
- setRange(double) - Method in class etomica.potential.P2ReactionFieldDipole
-
- setRange(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- setRatio(double, double) - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- setRawData(AccumulatorAverageBlockless.AllData) - Method in class etomica.data.AccumulatorAverageBlockless
-
- setRawData(AccumulatorAverageBlockless.AllData) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- setRCut(double) - Method in class etomica.potential.EwaldSummation
-
Sets a new value of rCutRealES
This will not alter values of alpha or nRealShells!
- setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- setrdfdr(double[]) - Method in class etomica.virial.HypernettedChain
-
- setrdfdr(double[]) - Method in class etomica.virial.PercusYevick
-
- setrdudr(double[]) - Method in class etomica.virial.PercusYevick1QC
-
- setRe(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setRe(double) - Method in class etomica.potential.P2Morse
-
- setReader(ConsoleReader) - Method in interface etomica.graph.engine.Console
-
- setReader(ConsoleReader) - Method in class etomica.graph.engine.ConsoleUI
-
- setRef(Quaternion) - Method in class org.jmol.util.Quaternion
-
- setRefAvg(DataOverlap.DataSourceOverlapAvg) - Method in class etomica.overlap.DataOverlap
-
- setReferenceDataInterval(int) - Method in class etomica.normalmode.SimOverlapModule
-
- setReferenceFracSource(IntegratorOverlap.ReferenceFracSource) - Method in class etomica.overlap.IntegratorOverlap
-
Sets the DataSource that retrieves data from both boxes and provides
information to the integrator about their progress, which is used to
decide how much to sample each system.
- setReflecting(boolean[]) - Method in class etomica.lattice.IndexIteratorReflecting
-
Indicates the indexes of the elements that are subject to reflection.
- setRefPref(double, double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- setRefPref(double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- setRefPref(double, double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- setRefPref(double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- setRefPref(double, double) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- setRefPref(double, double) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- setRefPref(double) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- setRefPref(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- setRefPref(double) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- setRefPref(double) - Method in class etomica.normalmode.MeterSamplingHarmonic
-
- setRefPref(double) - Method in class etomica.normalmode.MeterSamplingTarget
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- setRefPref(double) - Method in class etomica.normalmode.SimBennet
-
- setRefPref(double) - Method in class etomica.normalmode.SimHarmonicUmbrella
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlap
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlap
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapLJ
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapLJ
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- setRefPref(double) - Method in class etomica.normalmode.SimTargetUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.SimUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.SimUmbrellaSoftSphere
-
- setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setRefStepFraction(double) - Method in class etomica.overlap.IntegratorOverlap
-
- setRejectable(boolean) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setRelaxAction(MoleculeAction) - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- setRelaxAction(MoleculeAction) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- setRelaxationRateH(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setRelaxationRateP(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setRemove(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpecies1(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpecies2(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpecies3(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpeciesAfterAlertFlag(boolean) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setRepaintInterval(int) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- setRepaintSleep(int) - Method in class etomica.graphics.SimulationGraphic
-
- setRepeatCurrentAction(boolean) - Method in class etomica.action.activity.Controller
-
Flag indicating whether the current action should be repeated indefinitely before
moving on to the next action.
- setRescalingToFitVolume(boolean) - Method in class etomica.config.ConfigurationLattice
-
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
- setRescalingToFitVolume(boolean) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
- setRescalingToFitVolume(boolean) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
- setReservoirSize(int) - Method in class etomica.atom.AtomLeafAgentManager
-
Sets the size of the manager's "reservoir".
- setReservoirSize(int) - Method in class etomica.atom.MoleculeAgentManager
-
Sets the size of the manager's "reservoir".
- setReset(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setReset(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setResetAction(IAction) - Method in class etomica.graphics.DeviceNSelector
-
- setResidual(boolean) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets flag specifying if full or residual chemical potential is computed
Default is true (only residual is computed)
- setResidual(boolean) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setResizable(boolean) - Method in class etomica.graphics.DisplayCanvas
-
- setResizable(boolean) - Method in class etomica.graphics.DisplayPolytope
-
- setResizeOnNewBox(boolean) - Method in class etomica.graphics.DisplayBox
-
Set the flag indicating whether the graphic should resize from its
currently displayed size when a new box is set.
- setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
-
- setRm(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setRmax(double) - Method in class etomica.data.meter.MeterDihedralAngle
-
- setRmax(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setRmSquared(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setRotationAxis(IVector, double) - Method in class etomica.space3d.RotationTensor3D
-
Sets the tensor for rotation about the axis v by an angle theta.
- setRotationAxisCT(IVector, double) - Method in class etomica.space3d.RotationTensor3D
-
- setRotationBOTTOM(int, double) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- setRotationMatrix(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
-
- setRotationScale(Matrix3f) - Method in class org.jmol.util.Matrix4f
-
Replaces the upper 3x3 matrix values of this matrix with the values in the
matrix m1.
- setRotationTOP(int, double) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by
the given angle.
- setRotNum(int) - Method in class etomica.dimer.IntegratorDimerRT
-
- setRoute(int) - Method in class etomica.action.IntegratorDimerApproach
-
- setRoute(boolean) - Method in class etomica.virial.HypernettedChain
-
- setRoute(boolean) - Method in class etomica.virial.PercusYevick
-
- setRouteParams(double[][]) - Method in class etomica.action.IntegratorDimerApproach
-
- setRow(int, float, float, float) - Method in class org.jmol.util.Matrix3f
-
Sets the specified row of this matrix3d to the three values provided.
- setRow(int, float[]) - Method in class org.jmol.util.Matrix4f
-
Sets the specified row of this matrix4f to the four values provided.
- setRowA(int, float[]) - Method in class org.jmol.util.Matrix3f
-
Sets the specified row of this matrix3d to the four values provided.
- setRowHeaders(String[]) - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Sets the row headers.
- setRowLabelColumnHeader(String) - Method in class etomica.graphics.DisplayTable
-
Sets the header of the row-label column.
- setRowLabels(String[]) - Method in class etomica.graphics.DisplayTable
-
Sets values for descriptive text for each row (as defined before
transpose).
- setRowV(int, Vector3f) - Method in class org.jmol.util.Matrix3f
-
Sets the specified row of this matrix3d to the Vector provided.
- setRPow(double) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- setRun(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRun(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setS(int) - Static method in class etomica.potential.P2O2Bartolomei
-
- setSafetyFactor(double) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the safety factor (between 0 and 1.0) that determines when the
criterion thinks it needs an update.
- setSafetyFactor(double) - Method in class etomica.nbr.CriterionSimple
-
- setSafetyFactor(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Sets the safety factor.
- setSafetyFactor(double) - Method in class etomica.nbr.list.PotentialMasterList
-
Sets the safety factor.
- setSafetyFactor(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setSameFileEachTime(boolean) - Method in class etomica.data.DataLogger
-
Write to the same file at each time INTERVAL, and close the file at the
end of the simulation.
- setSampleClusters(ClusterWeight[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setSampledSwitchFrac(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setSaveValues(JButton) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- setScale(double) - Method in class etomica.action.BoxInflate
-
Sets the scale defining the amount of inflation.
- setScale(double) - Method in class etomica.graphics.DisplayBox
-
- setScale(double) - Method in class etomica.graphics.DisplayPolytope
-
- setScale(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a scale matrix with the passed scale
amount.
- setSCF(boolean) - Method in class etomica.potential.P2QChemInterpolated
-
- setSearchLimit(int) - Method in class etomica.kmc.IntegratorKMC
-
- setSecurityOff(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets whether or not scripts should be run securely
- setSeed(long) - Method in class etomica.util.MersenneTwister
-
Initalize the pseudo random number generator.
- setSeed(long) - Method in class etomica.util.MersenneTwisterFast
-
Initalize the pseudo random number generator.
- setSeed(int) - Method in class etomica.util.RandomMersenneTwister
-
Configures the RNG with the given seed.
- setSeedArray(int[]) - Method in class etomica.util.RandomMersenneTwister
-
Configures the RNG with an array of seeds
- setSeeds(int[]) - Method in class etomica.virial.simulations.SimulationVirial
-
- setSeen(int) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setSelected(String) - Method in class etomica.graphics.DeviceButtonGroup
-
Selects the button with the given label.
- setSelected(int) - Method in class etomica.graphics.DeviceButtonGroup
-
Selects ith radio button.
- setSelected(int) - Method in class etomica.graphics.DeviceSelector
-
Sets the i-th item (counting from 0) in the list as the one currently selected.
- setSelected(int) - Method in class etomica.graphics.DeviceThermoSelector
-
Sets the i-th item (counting from 0) in the list as the one currently selected.
- setSelectedFloats(float, BitSet, float[]) - Static method in class org.jmol.util.Parser
-
- setSelectedSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSelectedValue(int, ScriptVariable) - Method in class org.jmol.script.ScriptVariable
-
- setShakeTolerance(double) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setShape(Shape) - Method in class etomica.atom.AtomFilterInShape
-
- setShape(Polytope) - Method in class etomica.data.meter.MeterLocalDensity
-
- setShape(Polytope) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Sets the subvolume shape for the mole fraction calculation.
- setShape(String) - Method in class etomica.graphics.DeviceTrioControllerButton
-
Sets display shape of the device.
- setShapeOrigin(IVector) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Sets the origin of the subvolume (Polytopes typically have their center
at 0).
- setShearRateNumber(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setShift(IVector) - Method in class etomica.interfacial.WriteConfigurationInterfacial
-
- setShiftX(float) - Method in class etomica.graphics.DisplayCanvas
-
- setShiftY(float) - Method in class etomica.graphics.DisplayCanvas
-
- setShowBorder(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setShowBorder(boolean) - Method in class etomica.graphics.DeviceSpinner
-
- setShowBoundary(boolean) - Method in class etomica.graphics.DisplayBox
-
Set the flag indicating if the boundary should be drawn.
- setShowEValvalues(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set whether the eigenvalue # text box should be displayed.
- setShowingColumnHeaders(boolean) - Method in class etomica.graphics.DisplayTable
-
- setShowingRowLabels(boolean) - Method in class etomica.graphics.DisplayTable
-
Mutator method for whether table should include a column of "x" values.
- setShowingUnits(boolean) - Method in class etomica.graphics.DisplayTable
-
Flag indicating whether a units suffix applied to the column headers (or
row labels, if transposing).
- setShowSlider(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setShowValues(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setShowValues(boolean) - Method in class etomica.graphics.DeviceTernarySelector
-
Mutator method for flag indicating whether a set of boxes is
displayed with labels and fraction values as text.
- setShowValues(boolean) - Method in class etomica.graphics.DeviceThermoSlider
-
Set whether the temperature text box should be displayed.
- setShowValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set whether the temperature text box should be displayed.
- setShowValues(boolean) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set whether the x- and y-Cell # text box should be displayed.
- setShowValues(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set whether the wavevector # text box should be displayed.
- setSideLength(int) - Method in class etomica.graphics.DeviceTernarySelector
-
Mutator method for the length of each side of the triangle, in pixels.
- setSigma(double) - Method in class etomica.graphics.ColorSchemeOverlap
-
- setSigma(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setSigma(double) - Method in class etomica.modules.adsorption.P1Wall
-
- setSigma(double) - Method in class etomica.modules.colloid.P1Wall
-
- setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
Sets the radius.
- setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
Sets the radius.
- setSigma(double) - Method in class etomica.modules.sam.P1WCAWall
-
Sets the radius.
- setSigma(double) - Method in class etomica.modules.vle.VLESim
-
- setSigma(double) - Method in class etomica.potential.P1HardPeriodic
-
- setSigma(double) - Method in class etomica.potential.P22CLJQ
-
- setSigma(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
- setSigma(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeReference
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HSDipole
-
- setSigma(double) - Method in class etomica.potential.P2LennardJones
-
Mutator method for Lennard-Jones size parameter.
- setSigma(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
Mutator method for Lennard-Jones size parameter.
- setSigma(double) - Method in class etomica.potential.P2LJDipole
-
- setSigma(double) - Method in class etomica.potential.P2LJQ
-
- setSigma(double) - Method in class etomica.potential.P2LJQQ
-
- setSigma(double) - Method in class etomica.potential.P2SoftSphere
-
Mutator method for soft sphere size parameter.
- setSigma(double) - Method in class etomica.potential.P2WCA
-
Mutator method for Lennard-Jones size parameter.
- setSigma(double) - Method in class etomica.rotation.P2LJDipole
-
- setSigma(double) - Method in class etomica.units.systems.LJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setSigma(double) - Method in class etomica.virial.MayerEHardSphere
-
Sets the HS diameter.
- setSigma(double) - Method in class etomica.virial.MayerHardSphere
-
Sets the HS diameter.
- setSigma(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
- setSigmaColloid(double) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setSigmaHSRef(double, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setSigmaHSRefField(JTextField, int) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- setSigmaMonomer(double) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setSimEnvController(ControllerSimEnvironmentSelection) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- setSimulation(ISimulation, ISpace) - Method in class etomica.action.SimulationActionAdapter
-
- setSimulation(ISimulation, ISpace, IController) - Method in class etomica.action.SimulationRestart
-
- setSimulation(ISimulation) - Method in class etomica.box.BoxAgentManager
-
Sets the Simulation containing Boxs to be tracked.
- setSimulation(ISimulation, ISpace, Controller) - Method in class etomica.graphics.DeviceTrioControllerButton
-
Sets the controller that is toggled by this device.
- setSite(int[]) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Identifies the site whose neighbors will be given on iteration.
- setSite(String) - Method in enum etomica.virial.GUI.models.EnumSiteName
-
- setSiteFactor(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setSitesOnSpecies(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSize(int, int) - Method in class etomica.graphics.DeviceTable
-
Set the size attribute of the scrolled window the table sits on.
- setSize(int, int) - Method in class etomica.graphics.DisplayPlot
-
Sets the drawn size of the plot
- setSize(int, int) - Method in class etomica.graphics.DisplayPolytope
-
- setSize(double[]) - Method in class etomica.lattice.crystal.Primitive
-
Sets the length of each primitive vector to the corresponding
value in the given array.
- setSize(int[]) - Method in interface etomica.lattice.FiniteLattice
-
Sets the array size, defined as described in the getSize method.
- setSize(int) - Method in class etomica.lattice.IndexIteratorRectangular
-
Sets range of all indexes to the given value
Indices returned vary from 0 to size-1
- setSize(int[]) - Method in class etomica.lattice.IndexIteratorRectangular
-
Sets the individual ranges for the elements of the returned
array.
- setSize(int[]) - Method in interface etomica.lattice.IndexIteratorSizable
-
Specifies maximum index in each dimension (for dimension
i, maximum index is size[i]-1).
- setSize(int[]) - Method in class etomica.lattice.RectangularLattice
-
Sets the number lattice size (specified via the largest index in each dimension), and
rebuilds the all sites using the site factory.
- setSize(int, int) - Method in class etomica.modules.clustergenerator.Plot
-
Sets width and height of plot in pixels.
- setSize(int[]) - Method in interface g3dsys.control.IndexIterator
-
Sets the size of each dimension; in general they should all be the
same size.
- setSize(int) - Method in class org.jmol.util.Quadric
-
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
Sets A to the given value and B to 2.0/sqrt(3.0)*A
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- setSizeABC(double) - Method in class etomica.lattice.crystal.PrimitiveCubic
-
Sets the length of all primitive vectors to the given value.
- setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setSlab(double) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Set slab percentage
- setSlab(double) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Set slab percentage
- setSlab(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setSlab(BitSet, BitSet, String, String, float) - Method in class org.jmol.util.MeshSurface
-
- setSlabEnabled(boolean) - Method in class g3dsys.control.TransformManager
-
Enable/disable slab and depth
- setSlabPercent(float) - Method in class g3dsys.control.G3DSys
-
- setSleepPeriod(int) - Method in class etomica.action.activity.ActivityIntegrate
-
Sets amount of time that thread is kept in sleep state after
each doStep done on integrator.
- setSliderMajorValues(int) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the number of "major" values that should be shown on the
temperature slider.
- setSliderMajorValues(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the number of "major" values that should be shown on the
temperature slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the number of "major" values that should be shown on the
n- CellNum slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the number of "major" values that should be shown on the
x- and y- CellNum slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the number of "major" values that should be shown on the
eigenvalue slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the number of "major" values that should be shown on the
temperature slider.
- setSliderMinorValues(int) - Method in class etomica.graphics.DeviceThermoSlider
-
- setSliderPostAction(IAction) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the post slider value changed action.
- setSliderPostAction(IAction) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the post slider value changed action.
- setSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the post slider value changed action.
- setSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the post slider value changed action.
- setSliderTextboxesEditable(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
- setSliderValueShape(String) - Method in class etomica.graphics.DeviceSlider
-
- setSliderVerticalOrientation(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setSlitDim(int) - Method in class etomica.space.BoundaryRectangularSlit
-
Sets the non-periodic dimension to that indicated by the given value
(0 is x-dimension, 1 is y-dimension, etc.).
- setSmoothedY(double[]) - Method in class etomica.util.numerical.AkimaSplineSmoother
-
- setSnapshotTime(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the document time to seek to before rasterizing.
- setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSolventThermoFrac(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
Sets the fraction of well energy that is gained by an atom pair when
they hop in their well.
- setSources(String[]) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the list of individual SVG sources.
- setSpace(ISpace) - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory
-
Sets the Space
- setSpace(ISpace) - Method in class etomica.data.types.DataVector.DataInfoVectorFactory
-
Sets the Space
- setSpacePosition(double) - Method in class etomica.lattice.LatticePlane
-
Sets the position of the plane to be the given distance from the
origin in the direction of the normal.
- setSpecies(ISpecies) - Method in interface etomica.api.IAtomType
-
- setSpecies(ISpecies) - Method in class etomica.atom.AtomSourceRandomSpecies
-
- setSpecies(ISpecies) - Method in class etomica.atom.AtomTypeLeaf
-
- setSpecies(ISpecies) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
Sets the ISpecies for which the chemical potential is to be measured.
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterDensity
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Accessor method to set which species mole-fraction or molar-density is averaged
To set to total number density, invoke with static ALL_SPECIES field as argument
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterMoleFraction
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterNMolecules
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterProfileByVolume
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
- setSpecies(ISpecies[]) - Method in class etomica.dimer.PotentialMasterListDimer
-
- setSpecies(ISpecies) - Method in class etomica.graphics.DeviceNSelector
-
- setSpecies(ISpecies) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- setSpecies(ISpecies[]) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Mutator method for the set of species that can participate in an exchange move.
- setSpecies(ISpecies) - Method in class etomica.interfacial.WriteConfigurationInterfacial
-
- setSpecies(ISpecies) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
- setSpecies(ISpecies) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
- setSpecies(ISpecies, ISpecies) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setSpecies(ISpecies) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setSpecies(ISpecies) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- setSpecies(ISpecies) - Method in class etomica.modules.adsorption.MyMCMove
-
- setSpecies(ISpecies, ISpecies) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- setSpecies(ISpecies[]) - Method in class etomica.modules.chainequilibrium.MeterConversion
-
- setSpecies(ISpecies) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- setSpecies(String) - Method in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
-
- setSpecies(ISpecies[]) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setSpecies(ISpecies, ISpecies) - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- setSpecies(ISpecies) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- setSpecies(ISpecies) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- setSpecies(ISpecies, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- setSpecies1(ISpecies) - Method in class etomica.config.ConfigurationZincblende
-
- setSpecies1AtomicFlag(boolean) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- setSpecies2(ISpecies) - Method in class etomica.config.ConfigurationZincblende
-
- setSpecies2AtomicFlag(boolean) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- setSpeciesA(ISpecies, ISpecies) - Method in class etomica.config.GrainBoundaryConfiguration
-
- setSpeciesA(ISpecies) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- setSpeciesAllocation(ISpecies, float) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
Sets the initial allocation of the species on the left side
of the plane.
- setSpeciesAlreadyAdded(boolean, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesB(ISpecies, ISpecies) - Method in class etomica.config.GrainBoundaryConfiguration
-
- setSpeciesColloid(ISpecies) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setSpeciesCount1(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesCount2(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesCount3(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesDataModel(IMolecularModel_SpeciesFactory, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpeciesDM(ModelSelectedSpecies) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setSpeciesIdentifier(String, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setSpeciesIndex(int[]) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setSpeciesIndex(int, int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- setSpeciesIndex(int[]) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- setSpeciesIndex(int, int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- setSpeciesInteractionIndex(int[][]) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpeciesJList(JList) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesJList(JList) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesMembrane(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSpeciesMembrane(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesMoleculeCount(int, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpeciesMonomer(ISpecies) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setSpeciesRemovalMsgBox(JOptionPane) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesSelectedIndex(int[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesSelectedIndex(int, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesSelectionChanged(boolean) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesSelectionDM(ModelSpeciesSelection) - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- setSpeciesSolute(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSpeciesSolute1(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesSolute2(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesSolvent(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSpeciesSolvent(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesSpheres(SpeciesSpheresMono[]) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- setSpeciesTube(SpeciesTube) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- setSpecular(boolean) - Static method in class org.jmol.util.GData
-
- setSpecularExponent(int) - Static method in class org.jmol.util.GData
-
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of
shades
- setSpecularPercent(int) - Static method in class org.jmol.util.GData
-
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything,
really
- setSpecularPower(int) - Static method in class org.jmol.util.GData
-
fractional distance to white for specular dot
- setSpiffiness(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- setSpinnerPanel(JPanel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpringConstant(double) - Method in class etomica.modules.materialfracture.P1Tension
-
- setSpringConstant(double) - Method in class etomica.potential.P1Harmonic
-
- setSpringConstant(double) - Method in class etomica.potential.P1HarmonicSite
-
- setSpringConstant(double) - Method in class etomica.potential.P2Anharmonic
-
Accessor method for harmonic energy parameter
- setSpringConstant(double) - Method in class etomica.potential.P2Harmonic
-
Accessor method for harmonic energy parameter
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setStart(Object) - Method in class etomica.data.DataStreamAction
-
- setStart(float, float, float) - Method in class g3dsys.images.Line
-
- setStartAtom(int) - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- setStartConnection(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
- setStartMolecule(int) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- setState(boolean) - Method in class etomica.graphics.DeviceCheckBox
-
Sets the button to the given state.
- setState(boolean) - Method in class etomica.graphics.DeviceToggleButton
-
Toggles the button to the given state.
- setState(boolean) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Sets the button to the given state.
- setStationary(boolean) - Method in class etomica.potential.P1HardMovingBoundary
-
- setStepFactor(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setStepFreq0(double) - Method in class etomica.virial.overlap.IntegratorOverlap
-
- setStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- setStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveStep
-
- setStepSize(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Sets the step size of the move.
- setStepSizeMax(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- setStepSizeMax(double) - Method in class etomica.integrator.mcmove.MCMoveStep
-
- setStepSizeMax(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Sets the maximum allowable step size.
- setStepSizeMin(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- setStepSizeMin(double) - Method in class etomica.integrator.mcmove.MCMoveStep
-
- setStepSizeMin(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Returns the maximum allowable steps size.
- setStiffness(double, P1IntraMolecular) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setStiffness(double, double) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
Set PI harmonic spring stiffness for given temperature and atomic mass.
- setStopConnection(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
- setStopSimulation(boolean) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setSubDataInfo(IDataInfo[]) - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- setSubtractComb(boolean) - Method in class etomica.normalmode.DataSourceFE
-
If true, the free energy differences will not include the combinatoric
contributions (they will be the free energy of defect formation).
- setSulfurType(IAtomType) - Method in class etomica.modules.sam.IntegratorVelocityVerletSAM
-
- setSum(int) - Method in class etomica.math.discrete.FixedSumIterator
-
Specifies the target sum that defines the iterates.
- setSurfaceColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- setSurfaceDimension(int) - Method in class etomica.data.DataProcessorInterfacialTension
-
Sets the dimension of the surfaces.
- setSurfaceYOffset(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setSurfaceYOffset(double) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setSwitch(boolean) - Method in class etomica.models.nitrogen.PRotConstraint
-
- setSwitchFac(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- setSwitchFac(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- setSymbols(String[]) - Method in class etomica.graphics.DeviceTernarySelector
-
Symbols used to label each vertex of the triangle.
- setSystemSigmaHSRef(double) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setT(Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the value of the Tuple3f argument.
- setT(Tuple3i) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to the value of tuple t1.
- setT1(double) - Method in class etomica.normalmode.HTTPSoftSphereApplet
-
- setT2(double) - Method in class etomica.normalmode.HTTPSoftSphereApplet
-
- setTA(Tuple3f, float) - Method in class org.jmol.util.Quaternion
-
q = (cos(theta/2), sin(theta/2) * n)
- setTableColumnNames(String[]) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the column headers to the given strings and fires an event
indicating the column headers have been changed.
- setTableUpdateInterval(int) - Method in class etomica.data.DataTableAverages
-
Sets the interval for updating the table.
- setTags(DataTag[]) - Method in class etomica.data.DataInfoFactory
-
- setTags(DataTag[]) - Method in interface etomica.data.IEtomicaDataInfoFactory
-
Sets the factory's tags to those in the given array.
- setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIndexList
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntergroup
-
Specifies a target atom, which should appear in all iterates.
- setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntragroup
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Sets the target of iteration...
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Method to specify a target atom.
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Method to specify a target atom.
- setTarget(IAtom) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
Sets the target of iteration...
- setTarget(IAtom) - Method in interface etomica.atom.iterator.AtomsetIteratorTargetable
-
- setTarget(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorAll
-
Sets the target of iteration...
- setTarget(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorMolecule
-
Specifies molecule returned by this iterator, as the one containing
the given target atom.
- setTarget(IMolecule) - Method in interface etomica.atom.iterator.MoleculesetIteratorTargetable
-
- setTarget(IMolecule) - Method in class etomica.atom.iterator.MpiInterspecies1A
-
Sets the target molecule with which all pairs are formed.
- setTarget(IMolecule) - Method in class etomica.atom.iterator.MpiIntraspecies1A
-
Sets the target molecule with which all pairs are formed.
- setTarget(IMolecule) - Method in class etomica.atom.iterator.MpiMolecule
-
Sets target atoms and determines the pair iterator according to the value
of targetAtom.
- setTarget(IAtom) - Method in class etomica.atom.iterator.TripletInnerSequential
-
- setTarget(IAtom) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setTarget(IMolecule) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setTarget(IAtom) - Method in class etomica.nbr.cell.Api1ACell
-
Sets the target molecule with which all pairs are formed.
- setTarget(IMolecule) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Sets the target molecule with which all pairs are formed.
- setTarget(IAtom) - Method in class etomica.nbr.site.Api1ASite
-
Sets the target molecule with which all pairs are formed.
- setTarget(IAtom) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- setTarget(IMolecule) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- setTargetAtom(IAtom) - Method in class etomica.atom.iterator.IteratorDirective
-
- setTargetAtom(IAtom) - Method in interface etomica.potential.IPotential0Lrc
-
Informs the potential of a target atom.
- setTargetAtom(IAtom) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
-
- setTargetAtom(IAtom) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- setTargetAtom(IAtom) - Method in class etomica.potential.Potential0Lrc
-
- setTargetAvg(DataOverlap.DataSourceOverlapAvg) - Method in class etomica.overlap.DataOverlap
-
- setTargetDataInterval(int) - Method in class etomica.normalmode.SimOverlapModule
-
- setTargetDensity(double) - Method in class etomica.action.BoxInflate
-
Sets the action to change the box dimensions isotropically to achieve
the given density.
- setTargetH(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTargetMolecule(IMolecule) - Method in class etomica.atom.iterator.IteratorDirective
-
- setTargetMolecule(IMolecule) - Method in interface etomica.potential.IPotential0Lrc
-
Informs the potential of a target atom.
- setTargetMolecule(IMolecule) - Method in interface etomica.potential.IPotential0MoleculeLrc
-
Informs the potential of a target atom.
- setTargetMolecule(IMolecule) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
-
- setTargetMolecule(IMolecule) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- setTargetMolecule(IMolecule) - Method in class etomica.potential.Potential0Lrc
-
- setTargetP(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTargetT(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTemp(double) - Method in class etomica.integrator.IntegratorConNVT
-
- setTemperature(double) - Method in class etomica.action.AtomActionRandomizeVelocity
-
- setTemperature(double) - Method in class etomica.action.BoxQuench
-
Sets the quench temperature.
- setTemperature(double) - Method in class etomica.action.BoxRandomizeMomenta
-
- setTemperature(double) - Method in class etomica.action.BoxScaleMomenta
-
- setTemperature(double) - Method in class etomica.data.meter.MeterHyperVirial
-
- setTemperature(double) - Method in class etomica.data.meter.MeterPressure
-
- setTemperature(double) - Method in class etomica.data.meter.MeterPressureTensor
-
- setTemperature(double) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setTemperature(double) - Method in class etomica.densityofstate.DataProcessorPhi
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterBoltzmannA
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterBoltzmannB
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- setTemperature(double) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the current value for the temperature slider/text box.
- setTemperature(double) - Method in class etomica.integrator.IntegratorBox
-
Sets the temperature for this integrator
- setTemperature(double) - Method in class etomica.integrator.IntegratorHard
-
- setTemperature(double) - Method in class etomica.integrator.IntegratorMD
-
- setTemperature(double) - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- setTemperature(double) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
Sets the temperature so that chi can be compted in getA, avoiding
potential roundoff.
- setTemperature(double) - Method in class etomica.liquidLJ.MeterPU
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterPUCut
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedvirial.MappedUpotential
-
- setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- setTemperature(double, P2SoftSphericalTruncated) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- setTemperature(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setTemperature(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setTemperature(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setTemperature(double) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setTemperature(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setTemperature(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the current value for the temperature slider/text box.
- setTemperature(double) - Method in class etomica.normalmode.BoltzmannProcessor
-
- setTemperature(double) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- setTemperature(double) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
Sets the temperature being sampled.
- setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
Sets the temperature being sampled.
- setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
Sets the temperature being sampled.
- setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- setTemperature(double) - Method in class etomica.normalmode.MeterDDP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MeterDP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setTemperature(double) - Method in class etomica.normalmode.MeterSolidDA
-
- setTemperature(double) - Method in class etomica.normalmode.MeterSolidDACut
-
- setTemperature(double) - Method in class etomica.normalmode.MeterSolidMirror
-
- setTemperature(double) - Method in class etomica.normalmode.MeterTargetTP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- setTemperature(double) - Method in interface etomica.normalmode.NormalModes
-
Set the temperature used for calculating omega-squared.
- setTemperature(double) - Method in class etomica.normalmode.NormalModes1DHR
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModes2D
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModes3D
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesFromFile
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesMolecular
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesPotential
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setTemperature(double) - Method in class etomica.normalmode.WriteS
-
- setTemperature(double) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setTemperature(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setTemperature(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- setTemperature(double) - Method in class etomica.potential.P2LJDipole
-
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
- setTemperature(double) - Method in class etomica.potential.P2LJQ
-
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
- setTemperature(double) - Method in class etomica.potential.P2LJQQ
-
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
- setTemperature(double) - Method in class etomica.potential.P2SemiclassicalAtomic
-
- setTemperature(double) - Method in class etomica.potential.P2SemiclassicalMolecular
-
- setTemperature(double) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- setTemperature(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- setTemperature(double) - Method in class etomica.veos.VanderWaals
-
- setTemperature(double) - Method in interface etomica.virial.ClusterAbstract
-
- setTemperature(double) - Method in class etomica.virial.ClusterChainHS
-
- setTemperature(double) - Method in class etomica.virial.ClusterChainSoft
-
- setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlipped
-
- setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- setTemperature(double) - Method in class etomica.virial.ClusterDifference
-
- setTemperature(double) - Method in class etomica.virial.ClusterExchange
-
- setTemperature(double) - Method in class etomica.virial.ClusterSinglyConnected
-
- setTemperature(double) - Method in class etomica.virial.ClusterSum
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumHS
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizable
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- setTemperature(double) - Method in class etomica.virial.ClusterTree
-
- setTemperature(double) - Method in class etomica.virial.ClusterWeightAbs
-
- setTemperature(double) - Method in class etomica.virial.ClusterWeightSumWall
-
- setTemperature(double) - Method in class etomica.virial.ClusterWeightUmbrella
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyHS
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoft
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftBD
-
- setTemperature(double) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setTemperature(double) - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- setTemperature(double) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setTemperature(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setTemperature(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setTemperatureDataSource(DataSourceUniform) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
Sets the temperature data source to the one given.
- setTemperatures(double[]) - Method in class etomica.graphics.DeviceThermoSelector
-
- setTempZSlab(int) - Method in class org.jmol.g3d.Graphics3D
-
- setTetherLength(double) - Method in class etomica.potential.P2Tether
-
Accessor method for the tether distance
- setTextBackground(Color) - Method in class etomica.graphics.DeviceBox
-
- setThermalize(IntegratorBox, double, IRandom) - Method in class etomica.modules.adsorption.P1Wall
-
- setThermostat(IntegratorMD.ThermostatType) - Method in class etomica.integrator.IntegratorMD
-
Sets the type of thermostat used by the integrator.
- setThermostatInterval(int) - Method in class etomica.integrator.IntegratorMD
-
Sets the number of integrator intervals between thermostat
actions (for velocity scaling and Andersen thermostat).
- setThermostatNoDrift(boolean) - Method in class etomica.integrator.IntegratorMD
-
Configures the thermostat to remove any net momenta imparted
to the system.
- setTheta(double) - Method in class etomica.association.BiasVolumeSphereOriented
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.models.water.P2HardAssociationGCPMReference
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.models.water.PNWaterGCPMThreeSite
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeReference
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTheta(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setThetaFrac(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- setThickness(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setTHigh(double) - Method in class etomica.graphics.ColorSchemeTemperature
-
- setThreePoints(IVector, IVector, IVector) - Method in class etomica.math.geometry.Plane
-
Defines the plane by specifying three points that lie in it.
- setThreshold(int) - Method in class etomica.graphics.DeviceDelaySlider
-
You play with fire! This allows the slider to change not increase
the activity integrate sleep period, but also to decrease the integrator
timestep.
- setTilt(double) - Method in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
-
- setTilt(double) - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- setTime(double) - Method in class etomica.integrator.IntegratorAnalytic.AtomTimeAction
-
- setTimeDataSource(DataSourceScalar) - Method in class etomica.data.AccumulatorHistory
-
Sets the DataSource used for the "time" component of the history.
- setTimeStep(double) - Method in class etomica.integrator.IntegratorConNVT
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorGear4
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorMD
-
Sets integration time step.
- setTimeStep(double) - Method in class etomica.integrator.IntegratorVerlet
-
- setTimeStep(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setTitle(String) - Method in class etomica.graphics.AboutBoxWindow
-
- setTitle(String) - Method in class etomica.graphics.DeviceTable
-
Set the title of the border surrounding the table.
- setTitle(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
- setTLow(double) - Method in class etomica.graphics.ColorSchemeTemperature
-
- setToCenter(IVectorMutable) - Method in class etomica.math.geometry.Plane
-
Sets the given vector to be the point in the plane closest to the origin.
- setToInitialPosition(int[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- setToInitialPosition() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- setToInitialPosition(int[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- setToInitialPosition(double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- setToInPlaneSquare(IVector, double, IVectorMutable[]) - Method in class etomica.math.geometry.Plane
-
Returns four points as the vertices of a square of size d centered on x0.
- setToInPlaneSquare(double, IVectorMutable[]) - Method in class etomica.math.geometry.Plane
-
inPlaneSquare with square centered on point in plane closest to origin.
- setToInPlaneVectors(IVectorMutable[]) - Method in class etomica.math.geometry.Plane
-
Computes and returns two unit vectors perpendicular to each other and in the plane.
- setTolerance(double) - Method in class etomica.lattice.LatticePlane
-
- setTolerance(double) - Method in class etomica.modules.interfacial.FitTanh
-
- setTolerance(double) - Method in class etomica.surfacetension.FitTanh
-
- setTolerance(double) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- setToNearestPoint(IVector, IVectorMutable) - Method in class etomica.math.geometry.Plane
-
Determines the point in the plane closest to the point x0 (first argument).
- setToNormalVector(IVectorMutable) - Method in class etomica.math.geometry.Plane
-
Sets the given vector to be a unit normal vector to the plane and returns it.
- setTopPadding(double) - Method in class etomica.interfacial.ConfigurationLammps
-
- setTorqueSum(PotentialCalculationTorqueSum) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setTorsionpotentiala0(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala0(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTorsionpotentiala1(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala1(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTorsionpotentiala2(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala2(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTorsionpotentiala3(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala3(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTotalChildren(int) - Method in class etomica.modules.sam.SpeciesAlkaneThiol
-
- setTotalChildren(int) - Method in class etomica.species.SpeciesSpheresHetero
-
Sets the total number of child atoms created by this factory.
- setTotalChildren(int) - Method in class etomica.virial.SpeciesAlkane
-
- setToU(IMoleculeList, double[]) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- setToU(IMoleculeList, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setToU(IMoleculeList, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setToU(int, double, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- setToU(double[], IVectorMutable) - Method in class etomica.models.nitrogen.TestRotationVector
-
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinition
-
Set all the molecules in a cell to a position and orientation that corresponds to the
given generalized coordinate.
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionLeaf
-
Sets the position of the atom to be its lattice position plus the offset u
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- setToU(IMoleculeList, double[]) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setToUMoleculei(int, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setToUMoleculei(int, double[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setTracker(MCMoveTracker) - Method in class etomica.integrator.mcmove.MCMove
-
- setTransformationTensor(Tensor) - Method in class etomica.models.nitrogen.AtomActionTransformed
-
- setTransformationTensor(Tensor) - Method in class etomica.paracetamol.AtomActionTransformed
-
- setTranslation(Vector3f) - Method in class org.jmol.util.Matrix4f
-
Modifies the translational components of this matrix to the values of the
Vector3f argument; the other values of this matrix are not modified.
- setTranslationVector(IVector) - Method in class etomica.action.AtomActionTranslateBy
-
- setTranslucentCoverOnly(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setTransparentCursor(Object) - Method in interface org.jmol.api.ApiPlatform
-
- setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
-
- setTransposed(boolean) - Method in class etomica.graphics.DisplayTable
-
If fillHorizontal is true, each data set fills a row; if false, data are
arranged to fill columns.
- setTRatio(double) - Method in class etomica.virial.MeterVirialBDBin
-
- setTRatio(double) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setTRatio(double) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setTRatio(double) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setTriangle(DeviceTernarySelector.Triangle) - Method in class etomica.graphics.DeviceTernarySelector.MyEventManager
-
- setTrimThreshold(float) - Method in class etomica.atom.AtomArrayList
-
- setTrimThreshold(float) - Method in class etomica.atom.MoleculeArrayList
-
- setTrueLabel(String) - Method in class etomica.action.ActionToggle
-
Specifies the button's label when the toggle is set to true.
- setTrueLabel(String) - Method in class etomica.graphics.DeviceToggleButton
-
Specifies the button's label when the toggle is set to true.
- setTrueLabel(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Specifies the button's label when the toggle is set to true.
- setTruncation(double) - Method in class etomica.potential.PotentialGroupSoft
-
- setTruncationRadius(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2MoleculeTruncated
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftTruncated
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.rotation.P2LJDipole
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- setTSelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setTunable(boolean) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets a flag to indicate whether tuning of the move is to be performed
Tuning adjust the step size or other property of the move with the aim of
achieving a trial acceptance rate that is near to some target value.
- setType(char) - Method in interface etomica.graph.model.Edge
-
- setType(char) - Method in class etomica.graph.model.impl.EdgeImpl
-
- setType(char) - Method in class etomica.graph.model.impl.NodeImpl
-
- setType(char) - Method in interface etomica.graph.model.Node
-
- setTypeMax(DataSourceUniform.LimitType) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the type of the right limit.
- setTypeMin(DataSourceUniform.LimitType) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the type of the left limit.
- setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MeterDDP
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MeterDP
-
Sets a function that returns the lattice energy for a given density.
- setULatTruncFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
Sets a function that returns the lattice energy for a given density
using the same truncation as the potentials in the system.
- setUnit(Unit) - Method in class etomica.graphics.Device
-
- setUnit(Unit) - Method in class etomica.graphics.DeviceBox
-
Accessor method to set the physical units of the displayed value.
- setUnit(Unit) - Method in class etomica.graphics.DeviceSlider
-
Override superclass setUnit method to update label when unit is changed
- setUnit(Unit) - Method in class etomica.graphics.DeviceSpinner
-
Override superclass setUnit method to update label when unit is changed
- setUnit(PrefixedUnit) - Method in class etomica.graphics.DeviceThermoSelector
-
Override superclass setUnit method to update label when unit is changed
- setUnit(Unit) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the unit of temperature.
- setUnit(DataTag[], Unit) - Method in class etomica.graphics.DisplayPlot
-
- setUnit(Unit) - Method in class etomica.graphics.DisplayPlot
-
- setUnit(Unit) - Method in class etomica.graphics.DisplayScrollingGraph
-
Accessor method to set the physical units of the displayed value.
- setUnit(DataTag[], Unit) - Method in class etomica.graphics.DisplayTable
-
- setUnit(Unit) - Method in class etomica.graphics.DisplayTextBox
-
Accessor method to set the physical units of the displayed value.
- setUnit(Unit) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setUnit(Unit) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the unit of temperature.
- setUnit(Unit) - Method in interface etomica.units.Dimensioned
-
- setup(IBox, IPotentialMaster, IMoleculeList, ISpace) - Method in class etomica.action.CalcVibrationalModes
-
- setup() - Method in class etomica.dimer.IntegratorDimerMin
-
- setup() - Method in class etomica.dimer.IntegratorDimerRT
-
Takes in a current configuration of atoms (Rc) and creates a dimer of their positions (R1 and R2).
- setup() - Method in class etomica.dimer.IntegratorEnergyMap
-
- setup(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setup(byte, Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setup(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.Biconnected
-
- setup() - Method in class etomica.integrator.Integrator
-
Perform initialization.
- setup() - Method in class etomica.integrator.IntegratorManagerMC
-
- setup() - Method in class etomica.integrator.IntegratorMD
-
- setup() - Method in class etomica.kmc.IntegratorKMC
-
- setup() - Method in class etomica.kmc.IntegratorKMCCluster
-
- setup() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setup() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setup() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- setupActiveAtoms() - Method in class etomica.modules.adsorption.MyMCMove
-
- setupActiveAtoms() - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- setupBox() - Method in class etomica.atom.AtomLeafAgentManager
-
Sets the Box in which this AtomAgentManager will manage Atom agents.
- setupBox() - Method in class etomica.atom.MoleculeAgentManager
-
Sets the Box in which this AtomAgentManager will manage molecule agents.
- setupData(String, Dimension) - Method in class etomica.data.DataSourceFunction
-
Recalculates the y values from the current x values.
- setupData() - Method in class etomica.data.DataSourceRmsVelocity
-
Creates the data object (a DataFunction) to be returned by getData().
- setupData(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
Creates the data object (a DataFunction) to be returned by getData().
- setUpdateInterval(int) - Method in class etomica.graphics.DisplayTimer
-
Sets the period for updating the display.
- setUpdateInterval(int) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Sets the interval for which neighbor update checks are performed.
- setUpdateInterval(int) - Method in class etomica.nbr.list.NeighborListManager
-
Sets the interval for which neighbor update checks are performed.
- setUpdatingOnAnyChange(boolean) - Method in class etomica.data.DataSet
-
Describes protocol for firing table events that notify of column data
changes.
- setupIterators() - Method in class etomica.atom.iterator.ApiIntergroup
-
- setUpperTorsLimit(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setupProfileData() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- setupTargetHistogram() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Sets up a histogram for the target system that measures how often
maximum separation distances are visited.
- setuReactCO(double) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- setuReactCORev(double) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- setUseNbrLists(boolean) - Method in class etomica.nbr.PotentialMasterHybrid
-
- setUseNumberLocalization(boolean) - Static method in class org.jmol.util.TextFormat
-
- setUsePermutations(boolean) - Method in class etomica.virial.ClusterBonds
-
Sets the usePermutations flag.
- setUserStylesheet(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the user stylesheet.
- setUseSurfaceOnly(boolean) - Method in class etomica.modules.droplet.P2Cohesion
-
- setVA(Vector3f, float) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this AxisAngle4f to the specified axis and angle.
- setValidate(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Defines whether or not input sources should be validated in
the conversion process
- setValue(int) - Method in class etomica.graphics.DeviceBoxValueChangedEvent
-
Set the value of a DeviceBoxValueChangedEvent (should be the value of the text box)
- setValue(double) - Method in class etomica.graphics.DeviceSlider
-
- setValue(double) - Method in class etomica.graphics.DeviceSpinner
-
- setValue(Object) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Sets the value to the given value, which is taken to be in simulation units.
- setValue(double) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Sets the value to the given value, which is taken to be in simulation units.
- setValue(double) - Method in interface etomica.modifier.Modifier
-
Sets the value of the property.
- setValue(double) - Method in class etomica.modifier.ModifierFunctionWrapper
-
Applies function to given value before setting modified property.
- setValue(double) - Method in class etomica.modifier.ModifierGeneral
-
- setValue(double) - Method in class etomica.modifier.ModifierNMolecule
-
- setValue(double) - Method in class etomica.modules.adsorption.ModifierPMu
-
- setValue(double) - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- setValue(double) - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
-
- setValue(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
-
- setValue(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
-
- setValue(double) - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- setValue(double) - Method in class etomica.modules.entropylottery.ModifierDimensions
-
- setValue(double) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- setValue(double) - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- setValue(double) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- setValue(double) - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- setValue(double) - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.normalmode.ModifierCells3D
-
- setValue(double) - Method in class etomica.normalmode.ModifierXCells2D
-
- setValue(double) - Method in class etomica.normalmode.ModifierYCells2D
-
- setValue(Field, String) - Method in class etomica.util.ParameterBase
-
- setValue(Object, Field, String) - Method in interface etomica.util.ParameterParser
-
Sets obj's field to appropriate value based on the given string, if this
parser is appropriate for the given field, or throws an exception if
it's not.
- setValue(double) - Method in class etomica.virial.simulations.ModifierTPI
-
- setValueAt(Object, int, int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
Set the value in the given table cell.
- setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- setValueForAction(double) - Method in class etomica.modifier.ModifyAction
-
Stores the new value to be set by the wrapped modifier.
- setVaporColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- setVariable(String, Set<Graph>) - Method in interface etomica.graph.engine.Environment
-
- setVariable(String, Set<Graph>) - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- setVCut(double) - Method in class etomica.mappedvirial.MappedUpotential
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- setVectorScale(IVector) - Method in class etomica.action.BoxInflate
-
Sets the scale defining the amount of inflation for each dimension.
- setVertex1(IVector) - Method in class etomica.math.geometry.LineSegment
-
- setVertex2(IVector) - Method in class etomica.math.geometry.LineSegment
-
- setVFunc(PotentialCalculationMappedVirialV.VFunc) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- setViewSpeciesSelection(ViewSpeciesSelection) - Method in class etomica.virial.GUI.views.AppViewMixtureBuilder
-
- setVisible(boolean) - Method in class etomica.graph.viewer.ClusterViewer
-
- setVisible(boolean) - Method in class etomica.graphics.AboutBoxWindow
-
- setVMax(double) - Method in class etomica.graphics.DisplayScrollingGraph
-
- setVMin(double) - Method in class etomica.graphics.DisplayScrollingGraph
-
- setVolFluctuation(boolean) - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
- setVolume(double) - Method in class etomica.mappedvirial.MappedUpotential
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolumeBias(IFunction) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setVZero(double) - Method in class etomica.yukawa.P2Yukawa
-
- setW(double) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- setWallDim(int) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- setWallDim(int) - Method in class etomica.modules.sam.P1WCAWall
-
- setWallDim(int) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the orientation of the wall to be perpendicular to the given dimension
- setWallPosition(double) - Method in class etomica.modules.sam.P1WCAWall
-
- setWallPosition(double) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the position of the wall.
- setWallPosition(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setWallVelocity(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setWaveVec(IVectorMutable[]) - Method in class etomica.data.meter.MeterStructureFactor
-
- setWaveVector(IVector) - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.CalcJacobian
-
Sets the object that defines the normal-coordinate wave vectors.
- setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.MeterNormalMode
-
Sets the object that defines the normal-coordinate wave vectors.
- setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.WriteS
-
- setWaveVectorNum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the current value for the wavevector # slider/text box.
- setWaveVectorNum(int) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
Set the wave vectors used by the move.
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
Set the wave vectors that can be changed by the move.
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Set the wave vectors accessible to the move.
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterF
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setWaveVectors(IVectorMutable[]) - Method in class etomica.normalmode.MCMoveSingleMode
-
Set the wave vectors used by the move.
- setWaveVectors(IVectorMutable[], double[]) - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- setWaveVectors(IVectorMutable[], double[]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setWeight(Rational) - Method in class etomica.virial.cluster.ClusterDiagram
-
- setWeight(double) - Method in class etomica.virial.MeterVirialBDBin
-
- setWeight(double) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setWeight(double) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setWeight(double) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setWeightCoefficients(double[]) - Method in class etomica.virial.ClusterWeightUmbrella
-
- setWeightUpdateInterval(int) - Method in class etomica.tmmc.IntegratorTMMC
-
Sets the number of doStep calls between updating of weights.
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for attractive-well diameter divided by sigma;
- setWellDiameter(double) - Method in class etomica.potential.P2HardAssociation
-
Accessor for well-diameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for attractive-well depth parameter.
- setWidth(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
In less than or equal to zero, the width is not
constrained on the output image.
- setWidthHeight(boolean) - Method in class org.jmol.util.GData
-
- setWindow(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
Sets up a mapping from physical units to pixel units.
- setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
-
- setWireFrame(boolean) - Method in class g3dsys.images.ImageShell
-
- setWrappedPotential(PotentialHard) - Method in class etomica.potential.P2HardWrapper
-
- setWrappedPotential(IPotentialAtomic) - Method in class etomica.potential.P2MoleculeMonatomic
-
- setWriteInterval(int) - Method in class etomica.data.DataLogger
-
Define how many number of interval events received between writings to
file.
- setWriteInterval(int) - Method in class etomica.zeolite.MSDCoordWriter
-
Equates intervalAction method variable to variable passed in from simulation class
- setWriteOnFinish(IEtomicaDataSource) - Method in class etomica.data.DataLogger
-
- setWriteOnInterval(boolean) - Method in class etomica.data.DataLogger
-
- setWriteScale(boolean) - Method in class etomica.graphics.DisplayCanvas
-
- setWriteVelocity(boolean) - Method in class etomica.action.WriteConfigurationDLPOLY
-
- setWriteVelocity(boolean) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- setX(int, double) - Method in interface etomica.api.IVectorMutable
-
Sets the i-th component of the vector to the given value d.
- setX(double, double, int) - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
- setX(int, double) - Method in class etomica.space1d.Vector1D
-
- setX(int, double) - Method in class etomica.space2d.Vector2D
-
- setX(int, double) - Method in class etomica.space3d.Vector3D
-
- setX(int, double) - Method in class etomica.spaceNd.VectorND
-
- setX(float) - Method in class g3dsys.images.Ball
-
set the x molspace position of the figure
- setX(float) - Method in class g3dsys.images.Ellipse
-
set the x molspace position of the figure
- setX0(IVector) - Method in class etomica.potential.P1Harmonic
-
- setXCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the x-Cell # modifier object.
- setXCellNum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the current value for the xCell # slider/text box.
- setXComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the "x-axis" button to its selected state.
- setXDataSource(DataSourceIndependent) - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory
-
Sets array of independent DataInfo.
- setXFlipped(boolean) - Method in class g3dsys.control.G3DSys
-
- setXicom(double[]) - Method in class etomica.util.numerical.Function1d
-
- setXLabel(String) - Method in class etomica.graphics.DisplayPlot
-
- setXMax(double) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the right limit of the range.
- setXMin(double) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the left limit of the range.
- setXRange(double, double, int) - Method in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
Defines the region atoms must be selected from.
- setXRange(DoubleRange) - Method in interface etomica.util.Histogram
-
Sets the range of x values used in the histogram (min and max).
- setXRange(DoubleRange) - Method in class etomica.util.HistogramCollapsing
-
- setXRange(DoubleRange) - Method in class etomica.util.HistogramDiscrete
-
- setXRange(DoubleRange) - Method in class etomica.util.HistogramExpanding
-
- setXRange(DoubleRange) - Method in class etomica.util.HistogramNotSoSimple
-
- setXRange(DoubleRange) - Method in class etomica.util.HistogramReweightedData
-
- setXRange(DoubleRange) - Method in class etomica.util.HistogramSimple
-
- setXRot(float) - Method in class etomica.graphics.DisplayCanvas
-
- setXScale(double, double, double) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the minimum and maximum X-axis limits on the function display
sliders.
- setXSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the post slider value changed action.
- setXUnit(Unit) - Method in class etomica.graphics.DisplayPlot
-
Extend superclass method to update label with change of unit.
- setXYZChange() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setY(float) - Method in class g3dsys.images.Ball
-
set the y molspace position of the figure
- setY(float) - Method in class g3dsys.images.Ellipse
-
set the y molspace position of the figure
- setYCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the y-Cell # modifier object.
- setYCellNum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the current value for the yCell # slider/text box.
- setYComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the "y-axis" button to its selected state.
- setYesButton(JButton) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
-
- setYFlipped(boolean) - Method in class g3dsys.control.G3DSys
-
- setYRot(float) - Method in class etomica.graphics.DisplayCanvas
-
- setYScale(double, double, double) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the minimum and maximum Y-axis limits on the function display
sliders.
- setYScale(double) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- setYSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- setZ(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setZ(float) - Method in class g3dsys.images.Ball
-
set the z molspace position of the figure
- setZ(float) - Method in class g3dsys.images.Ellipse
-
set the z molspace position of the figure
- setZ1(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setZ2(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setZ3() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setZ4211() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setZ4220() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setZero() - Method in class org.jmol.util.Matrix3f
-
Sets this matrix to all zeros.
- setZero() - Method in class org.jmol.util.Matrix4f
-
Sets this matrix to all zeros.
- setZFraction(double, double) - Method in class etomica.modules.adsorption.MyMCMove
-
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
- setZFraction(double) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
- setZoom(float) - Method in class etomica.graphics.DisplayCanvas
-
- setZShade(boolean, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- setZShade(boolean, int, int, int) - Method in class org.jmol.util.GData
-
- sgn(double) - Static method in class etomica.math.SpecialFunctions
-
The sign function, returning -1 if x < 0, zero if x == 0, and +1 if x > 0.
- shadeIndexLast - Static variable in class org.jmol.util.Shader
-
- shadeIndexMax - Static variable in class org.jmol.util.Shader
-
- shadeIndexNoisyLimit - Static variable in class org.jmol.util.Shader
-
- shadeIndexNormal - Static variable in class org.jmol.util.Shader
-
- Shader - Class in org.jmol.util
-
All static functions.
- Shader() - Constructor for class org.jmol.util.Shader
-
- shakeAgentManager - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- shakeTol - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- Shape - Interface in etomica.math.geometry
-
Interface for an object that defines a closed region of space.
- shape - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- shape - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- shape - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- shape - Variable in class etomica.space.Boundary
-
- shape - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- shape - Static variable in class org.jmol.script.Token
-
- SHAPE_AXES - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_BALLS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_CARTOON - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_CONTACT - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_DOTS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_DRAW - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ECHO - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_FRANK - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_HALOS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_HOVER - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_LABELS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MEASURES - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MO - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_PMESH - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STARS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STICKS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STRANDS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STRUTS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_TRACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_VECTORS - Static variable in class org.jmol.viewer.JmolConstants
-
- shapeClassBases - Static variable in class org.jmol.viewer.JmolConstants
-
- ShapeData() - Constructor for class etomica.virial.simulations.ShapeParser.ShapeData
-
- ShapeParser - Class in etomica.virial.simulations
-
- ShapeParser() - Constructor for class etomica.virial.simulations.ShapeParser
-
- ShapeParser.ShapeData - Class in etomica.virial.simulations
-
- shapes - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- shapeTokenIndex(int) - Static method in class org.jmol.viewer.JmolConstants
-
- shareData - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- shareData - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- shearBox - Variable in class etomica.modules.rheology.RheologyGraphic
-
- shearRate - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- sheet - Static variable in class org.jmol.script.Token
-
- sheetsmoothing - Static variable in class org.jmol.script.Token
-
- shift - Variable in class etomica.interfacial.ConfigurationLammps
-
- shift - Variable in class etomica.interfacial.WriteConfigurationInterfacial
-
- shift - Variable in class etomica.metastable.MeterDensityDistribution
-
- shift - Variable in class etomica.models.co2.PNCO2GCPM
-
- shift - Variable in class etomica.models.co2.PNGCPM
-
- shift - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- shift - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- shift - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- shift - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- shift - Variable in class etomica.models.water.P2Water3P
-
- shift - Variable in class etomica.models.water.P2Water4P
-
- shift - Variable in class etomica.models.water.PNWaterGCPM
-
- shift(int) - Method in class etomica.modules.render.ParseObj.BondInfo
-
- shift - Variable in class etomica.potential.P2CO2EMP
-
- shift - Variable in class etomica.potential.P2SoftSphericalTruncatedShifted
-
- shift - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- shift0 - Variable in class etomica.space.BoundaryRectangular
-
- shift0 - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- shifted - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- shiftMomenta() - Method in class etomica.integrator.IntegratorMD
-
Subtracts velocity from all atoms such that the new net momentum of
the whole system is 0.
- shiftMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- show() - Method in class etomica.math.linearalgebra.Matrix
-
- showaxes - Static variable in class org.jmol.script.Token
-
- showBoundary - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- showboundbox - Static variable in class org.jmol.script.Token
-
- showfrank - Static variable in class org.jmol.script.Token
-
- showhiddenselectionhalos - Static variable in class org.jmol.script.Token
-
- showhydrogens - Static variable in class org.jmol.script.Token
-
- showingColumnHeaders - Variable in class etomica.graphics.DisplayTable
-
- showingRowLabels - Variable in class etomica.graphics.DisplayTable
-
- showingUnits - Variable in class etomica.graphics.DisplayTable
-
- showkeystrokes - Static variable in class org.jmol.script.Token
-
- showmeasurements - Static variable in class org.jmol.script.Token
-
- showmultiplebonds - Static variable in class org.jmol.script.Token
-
- shownavigationpointalways - Static variable in class org.jmol.script.Token
-
- showNumMoleculesPlots - Variable in class etomica.modules.vle.VLE
-
- showPlane - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- showPointInput(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the visibility of the data point input table.
- showReport(SimulationVirialOverlap2, IIntegratorListener) - Method in class etomica.virial.GUI.components.SimulationRunner
-
- showScale(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the visibility of the plot axis limit sliders.
- showscript - Static variable in class org.jmol.script.Token
-
- ShowStep - Class in etomica.models.hexane
-
- ShowStep() - Constructor for class etomica.models.hexane.ShowStep
-
- showtiming - Static variable in class org.jmol.script.Token
-
- showunitcell - Static variable in class org.jmol.script.Token
-
- sidechain - Static variable in class org.jmol.script.Token
-
- sig - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
-
- sig - Variable in class etomica.util.numerical.NonLinearCurveFitting
-
- sig - Variable in class etomica.virial.ClusterWheatleyHS.AllSigs
-
- sig - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- sig2 - Variable in class etomica.graphics.ColorSchemeOverlap
-
- sig2 - Variable in class etomica.potential.P2HardSphere
-
Square of collisionDiameter
- sigBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- sigBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sigBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- sigBox - Variable in class etomica.modules.swmd.SwmdGraphic
-
- sigCounter - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- sigma - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- sigma - Variable in class etomica.models.water.P2Water3P
-
- sigma - Variable in class etomica.models.water.P2Water4P
-
- sigma - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- sigma - Variable in class etomica.models.water.PNWaterGCPM
-
- sigma - Variable in class etomica.modules.adsorption.EOSSW
-
- sigma - Variable in class etomica.modules.adsorption.P1Wall
-
- sigma - Variable in class etomica.modules.colloid.P1Wall
-
- sigma - Variable in class etomica.modules.dcvgcmd.P1WCAWall
-
- sigma - Variable in class etomica.modules.droplet.DropletAtomic
-
- sigma - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- sigma - Variable in class etomica.modules.sam.P1WCAWall
-
- sigma - Variable in class etomica.modules.swmd.SwmdGraphic
-
- sigma - Variable in class etomica.modules.vle.VLESim
-
- sigma - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- sigma - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- sigma - Variable in class etomica.potential.P1HardPeriodic
-
- sigma - Variable in class etomica.potential.P2ElectrostaticWithHardCore
-
- sigma(double) - Method in class etomica.potential.P3HydrogenManzhos
-
- sigma - Variable in class etomica.units.systems.LJ
-
- sigma(int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate sigma(n).
- sigma(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate sigma(n).
- sigma() - Method in class etomica.veos.bigdecimal.Ifactor
-
Sum of the divisors of the number.
- sigma(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Sum of the k-th powers of divisors of the number.
- sigma - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomHSChain
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomHSTree
-
- sigma - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- sigma - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- sigma - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigma0point - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigma2 - Variable in class etomica.models.water.P2Water3P
-
- sigma2 - Variable in class etomica.models.water.P2Water4P
-
- sigma2 - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- sigma2 - Variable in class etomica.modules.sam.P1WCAWall
-
- sigma2 - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- sigma2 - Variable in class etomica.virial.MayerWell
-
- sigmaA - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaABpoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaAll - Variable in class etomica.models.co2.PNCO2GCPM
-
- sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaApoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaC - Variable in class etomica.models.co2.PNCO2GCPM
-
- sigmaC - Variable in class etomica.potential.P2CO2EMP
-
- sigmaC2 - Variable in class etomica.potential.P2CO2EMP
-
- sigmaCH2 - Variable in class etomica.modules.sam.Sam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaCO - Variable in class etomica.potential.P2CO2EMP
-
- sigmaCO2 - Variable in class etomica.potential.P2CO2EMP
-
- sigmaColloid - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- sigmaH - Variable in class etomica.models.water.PNWaterGCPM
-
- sigmaHC - Static variable in class etomica.potential.P2HePCKLJS
-
- sigmaHC2 - Variable in class etomica.potential.P2HeSimplified
-
- sigmaHS - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- sigmaHS - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- sigmaHS - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- sigmaHSRef - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.ReeHooverMC.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- sigmak(BigInteger, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate sigma_k(n).
- sigmaLJ - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- sigmaLJ - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- sigmaLJ - Variable in class etomica.dielectric.TIP4P_NVT
-
- sigmaM - Variable in class etomica.models.water.PNWaterGCPM
-
- sigmaMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sigmaMonomer - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- sigmaN - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- sigmaO - Variable in class etomica.models.co2.PNCO2GCPM
-
- sigmaO - Variable in class etomica.potential.P2CO2EMP
-
- sigmaO2 - Variable in class etomica.potential.P2CO2EMP
-
- sigmaOC - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- sigmaOH - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- sigmaSF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sigmaSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sign(double, double) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
-
- signature() - Method in class etomica.atom.Atom
-
Returns a string of digits that uniquely identifies this atom.
- signature() - Method in class etomica.atom.Molecule
-
Returns a string of digits that uniquely identifies this atom.
- signature() - Method in class etomica.units.Dimension
-
The signature is the exponents of each of the base dimensions forming the
given dimension.
- signatureMaker - Variable in class etomica.graph.iterators.filters.GlobalFilter
-
- SignatureMaker() - Constructor for class etomica.graph.iterators.filters.GlobalFilter.SignatureMaker
-
- signum() - Method in class etomica.veos.bigdecimal.BigSurd
-
The sign: 1 if the number is >0, 0 if ==0, -1 if <0
- signum() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Sign function.
- signum() - Method in class etomica.veos.bigdecimal.Rational
-
The sign: 1 if the number is >0, 0 if ==0, -1 if <0
- Silver - Class in etomica.chem.elements
-
Class for the Silver element.
- Silver(String) - Constructor for class etomica.chem.elements.Silver
-
- Silver(String, double) - Constructor for class etomica.chem.elements.Silver
-
- SILVER - Static variable in class org.jmol.util.Colix
-
- sim - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- sim - Variable in class etomica.atom.AtomTypeAgentManager
-
- sim - Variable in class etomica.atom.MoleculeAgentManager
-
- sim - Variable in class etomica.atom.SpeciesAgentManager
-
- sim - Variable in class etomica.box.BoxAgentSourceMoleculeManager
-
- sim - Variable in class etomica.data.meter.MeterKineticEnergyRigid
-
- sim - Variable in class etomica.data.meter.MeterTemperature
-
- sim - Variable in class etomica.dimer.IntegratorDimerMin
-
- sim - Variable in class etomica.dimer.IntegratorDimerRT
-
- sim - Variable in class etomica.graphics.DisplayBox
-
- sim - Variable in class etomica.integrator.IntegratorRigidIterative
-
- sim - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- sim - Variable in class etomica.modules.adsorption.AdsorptionGraphic
-
- sim - Variable in class etomica.modules.catalysis.CatalysisGraphic
-
- sim - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- sim - Variable in class etomica.modules.catalysis.ReactionManagerCO
-
- sim - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
-
- sim - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- sim - Variable in class etomica.modules.colloid.ColloidGraphic
-
- sim - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- sim - Variable in class etomica.modules.droplet.DropletAtomicGraphic
-
- sim - Variable in class etomica.modules.droplet.DropletGraphic
-
- sim - Variable in class etomica.modules.ensembles.LJMCGraphic
-
- sim - Variable in class etomica.modules.entropylottery.EntropyLotteryGraphic
-
- sim - Variable in class etomica.modules.insertion.InsertionGraphic
-
- sim - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- sim - Variable in class etomica.modules.ljmd.LjmdGraphic
-
- sim - Variable in class etomica.modules.mu.MuGraphic
-
- sim - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.multiharmonic.MultiharmonicGraphic
-
- sim - Variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.osmosis.Osmosis
-
- sim - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- sim - Variable in class etomica.modules.render.RenderMDGraphic
-
- sim - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- sim - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- sim - Variable in class etomica.modules.rosmosis.MeterFlux
-
- sim - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sim - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- sim - Variable in class etomica.modules.sam.ConfigurationSAM
-
- sim - Variable in class etomica.modules.sam.CriterionTether3
-
- sim - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- sim - Variable in class etomica.modules.swmd.SwmdGraphic
-
- sim - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- sim - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- sim - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- sim - Variable in class etomica.nbr.cell.NeighborCellManager
-
- sim - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- sim - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- sim - Variable in class etomica.normalmode.HTTPSoftSphereApplet
-
- sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- sim - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- sim - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- sim - Variable in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- SIM - Static variable in class etomica.units.systems.UnitSystem
-
- Sim() - Constructor for class etomica.units.systems.UnitSystem.Sim
-
- SIM_UNIT - Static variable in class etomica.units.Angle
-
- SIM_UNIT - Static variable in class etomica.units.Area
-
- SIM_UNIT - Static variable in class etomica.units.Charge
-
Simulation unit of charge.
- SIM_UNIT - Static variable in class etomica.units.Current
-
Simulation unit of electrical current.
- SIM_UNIT - Static variable in class etomica.units.Dipole
-
- SIM_UNIT - Static variable in class etomica.units.ElectricPotential
-
Simulation unit of charge.
- SIM_UNIT - Static variable in class etomica.units.Energy
-
The simulation unit of energy is D-A^2/ps^2.
- SIM_UNIT - Static variable in class etomica.units.Force
-
- SIM_UNIT - Static variable in class etomica.units.Fraction
-
The simulation unit is the Decimal.
- SIM_UNIT - Static variable in class etomica.units.Length
-
Simulation unit for length is the angstrom.
- SIM_UNIT - Static variable in class etomica.units.LuminousIntensity
-
The Candela unit.
- SIM_UNIT - Static variable in class etomica.units.Mass
-
The simulation unit is the Dalton.
- SIM_UNIT - Static variable in class etomica.units.Pressure
-
Simulation unit of pressure is (D-A/ps^2)/A^2 = D/(A-ps^2).
- SIM_UNIT - Static variable in class etomica.units.Pressure2D
-
- SIM_UNIT - Static variable in class etomica.units.Quantity
-
Simulation unit is Count.
- SIM_UNIT - Static variable in class etomica.units.Temperature
-
The simulation unit for temperature, which as kT has dimensions
of energy and is D-A^2/ps^2.
- SIM_UNIT - Static variable in class etomica.units.Time
-
Simulation unit for time is the picosecond.
- SIM_UNIT - Static variable in class etomica.units.Viscosity
-
The simulation unit is Dalton/(A-ps).
- SIM_UNIT - Static variable in class etomica.units.Volume
-
Simulation unit of volume is cubic Angstroms.
- SimBennet - Class in etomica.normalmode
-
Simulation to sample Bennet's Overlap Region
- SimBennet(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimBennet
-
- SimBennet.SimBennetParam - Class in etomica.normalmode
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimBennet.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimUmbrella.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- SimCalcJ - Class in etomica.normalmode
-
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.
- SimCalcJ(Space, int) - Constructor for class etomica.normalmode.SimCalcJ
-
- SimCalcS - Class in etomica.normalmode
-
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcS(Space, int, double) - Constructor for class etomica.normalmode.SimCalcS
-
- SIMCALCS - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- SIMCALCS - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- SimCalcSLJ - Class in etomica.normalmode
-
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSLJ(Space, int, double, double) - Constructor for class etomica.normalmode.SimCalcSLJ
-
- SimCalcSMorse - Class in etomica.normalmode
-
MC simulation of Morse model in 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSMorse(Space, int, double, double) - Constructor for class etomica.normalmode.SimCalcSMorse
-
- SimCalcSSoftSphere2D - Class in etomica.normalmode
-
MC simulation of FCC soft-sphere model in 2D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSSoftSphere2D(Space, int, int[], double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphere2D
-
- SimCalcSSoftSphereFCC - Class in etomica.normalmode
-
MC simulation of FCC soft-sphere model in 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSSoftSphereFCC(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphereFCC
-
- SimCalcSSoftSphereFCCSuperBox - Class in etomica.normalmode
-
MC simulation of FCC soft-sphere model in 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSSoftSphereFCCSuperBox(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- simCDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simCDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- simCDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simCDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimDegFreeBinning - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom
- SimDegFreeBinning(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimDegFreeBinning
-
- SimDegFreeBinning.SimParam - Class in etomica.models.oneDHardRods
-
- SimDegreeFreedom - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom
- SimDegreeFreedom(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom
-
- SimDegreeFreedom.SimParam - Class in etomica.models.oneDHardRods
-
- SimDegreeFreedom3D - Class in etomica.models.oneDHardRods
-
MC simulation
3D hard spheres
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom
- SimDegreeFreedom3D(Space, int, double, int, int, String) - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- SimDegreeFreedom3D.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImage - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Calculate free energy of solid
Treats modes as degrees of freedom; keeps one rod at each end that does not
move by central image.
- SimDifferentImage(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage
-
- SimDifferentImage.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImage1D - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Calculate free energy of solid
Treats modes as degrees of freedom; keeps one rod at each end that does not
move by central image.
- SimDifferentImage1D(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1D
-
- SimDifferentImage1D.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImage1DHR - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Calculate free energy of solid
Treats modes as degrees of freedom; keeps one rod at each end that does not
move by central image.
- SimDifferentImage1DHR(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- SimDifferentImage1DHR.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImageSsFcc - Class in etomica.models.oneDHardRods
-
MC simulation
3D Lennard Jones
FCC crystal
No graphic display
Uses wavevector approach
Calculate free energy of solid using normal mode insertion method
Treats coupling of modes as overlap variable;
Generate input files with HarmonicCrystalSoftSphereFCC
Uses overlap sampling.
- SimDifferentImageSsFcc(Space, int[], int[], double, int, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- SimDifferentImageSsFcc.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImageSsFccBigCell - Class in etomica.models.oneDHardRods
-
MC simulation
3D Lennard Jones
FCC crystal
No graphic display
uses single big cell approach
Calculate free energy of solid using normal mode insertion method
Treats coupling of modes as overlap variable;
Generate input files with HarmonicCrystalSoftSphereFCC
Uses overlap sampling.
- SimDifferentImageSsFccBigCell(Space, int[], int[], double, int, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- SimDifferentImageSsFccBigCell.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImageSsFccDoubleSize - Class in etomica.models.oneDHardRods
-
MC simulation
3D Lennard Jones
FCC crystal
No graphic display
uses single big cell approach
Calculate free energy of solid using normal mode insertion method
Treats coupling of modes as overlap variable;
Generate input files with HarmonicCrystalSoftSphereFCC
Uses overlap sampling.
- SimDifferentImageSsFccDoubleSize(Space, int[], int[], double, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- SimDifferentImageSsFccDoubleSize.SimParam - Class in etomica.models.oneDHardRods
-
- SimDimerLJadatom - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom on a surface, modeled with LJ.
- SimDimerLJadatom() - Constructor for class etomica.dimer.SimDimerLJadatom
-
- SimDimerLJadatomCluster - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerLJadatomCluster(Space) - Constructor for class etomica.dimer.SimDimerLJadatomCluster
-
- SimDimerLJgb - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerLJgb() - Constructor for class etomica.dimer.SimDimerLJgb
-
- SimDimerMEAMadatom - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMadatom() - Constructor for class etomica.dimer.SimDimerMEAMadatom
-
- SimDimerMEAMadatomCluster - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMadatomCluster(Space) - Constructor for class etomica.dimer.SimDimerMEAMadatomCluster
-
- SimDimerMEAMGB - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMGB(int[], int[]) - Constructor for class etomica.dimer.SimDimerMEAMGB
-
- SimDimerMEAMGBCluster - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMGBCluster(Space) - Constructor for class etomica.dimer.SimDimerMEAMGBCluster
-
- SimDirectBetaN2RP - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
- SimDirectBetaN2RP(Space, int, double, double, double[]) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RP
-
- SimDirectBetaN2RP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
- SimDirectBetaN2RPAngleToNoAngle - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
- SimDirectBetaN2RPAngleToNoAngle(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- SimDirectBetaN2RPInitPert - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
- SimDirectBetaN2RPInitPert(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- SimDirectDisorderedAlphaN2RPInitPert - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
- SimDirectDisorderedAlphaN2RPInitPert(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- simEigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simEigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimEinStep1 - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep1(Space, int, double, double, double, int, double, boolean) - Constructor for class etomica.normalmode.SimEinStep1
-
- SimEinStep1.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimEinStep1HCP - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep1HCP(Space, int, double, double, double, int, double, double) - Constructor for class etomica.normalmode.SimEinStep1HCP
-
- SimEinStep1HCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimEinStep2 - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep2(Space, int, double, double, double, int, double, boolean) - Constructor for class etomica.normalmode.SimEinStep2
-
- SimEinStep2.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimEinStep2.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimEinStep2HCP - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep2HCP(Space, int, double, double, double, int, double, double) - Constructor for class etomica.normalmode.SimEinStep2HCP
-
- SimEinStep2HCP.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimEinStep2HCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- simEventManager - Variable in class etomica.box.BoxAgentManager
-
- SimExtensiveTest - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Testing whether or not using modes as degrees of freedom is extensive.
- SimExtensiveTest(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimExtensiveTest
-
- SimExtensiveTest.SimParam - Class in etomica.models.oneDHardRods
-
- SimFluidSoftSphere - Class in etomica.normalmode
-
MC simulation of soft-sphere fluid model
- SimFluidSoftSphere(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimFluidSoftSphere
-
- simGraphic - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- SimHarmonic - Class in etomica.normalmode
-
Simulation to sample harmonic potential
- SimHarmonic(Space, int, double, String, double) - Constructor for class etomica.normalmode.SimHarmonic
-
- SimHarmonicHexane - Class in etomica.models.hexane
-
- SimHarmonicHexane(Space, double, int, int, int, String, double) - Constructor for class etomica.models.hexane.SimHarmonicHexane
-
- SimHarmonicUmbrella - Class in etomica.normalmode
-
Simulation to sample harmonic system and perturbing into
the umbrella sampling region
- SimHarmonicUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimHarmonicUmbrella
-
- SimHarmonicUmbrella.SimBennetParam - Class in etomica.normalmode
-
- SimHSMDVacancy - Class in etomica.normalmode
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimHSMDVacancy(int, double, double, int, int, double) - Constructor for class etomica.normalmode.SimHSMDVacancy
-
- SimHSMDVacancy.HSMDVParams - Class in etomica.normalmode
-
- SimIdealGas - Class in etomica.freeenergy.npath
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimIdealGas(int, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimIdealGas
-
- SimIdealGas.LjMC3DParams - Class in etomica.freeenergy.npath
-
- simImagT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simImagT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimKMCLJadatom - Class in etomica.kmc
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom on a surface, modeled with LJ.
- SimKMCLJadatom() - Constructor for class etomica.kmc.SimKMCLJadatom
-
- SimKMCmaster - Class in etomica.kmc
-
- SimKMCmaster(ISpace) - Constructor for class etomica.kmc.SimKMCmaster
-
- SimKMCMEAMadatom - Class in etomica.kmc
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimKMCMEAMadatom() - Constructor for class etomica.kmc.SimKMCMEAMadatom
-
- SimKMCworker - Class in etomica.kmc
-
- SimKMCworker(ISpace) - Constructor for class etomica.kmc.SimKMCworker
-
- SimLJ - Class in etomica.freeenergy.npath
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimLJ(int, double, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimLJ
-
- SimLJ.LjMC3DParams - Class in etomica.freeenergy.npath
-
- SimLJHTTISuper - Class in etomica.normalmode
-
- SimLJHTTISuper(Space, int, double, double, double, boolean, int[]) - Constructor for class etomica.normalmode.SimLJHTTISuper
-
- SimLJHTTISuper.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimLJHTTISuperHCP - Class in etomica.normalmode
-
- SimLJHTTISuperHCP(Space, int, double, double, double, double, boolean, int[]) - Constructor for class etomica.normalmode.SimLJHTTISuperHCP
-
- SimLJHTTISuperHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimLJVacancy - Class in etomica.normalmode
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimLJVacancy(int, double, double, double, int, double, boolean, boolean) - Constructor for class etomica.normalmode.SimLJVacancy
-
- SimLJVacancy.Applet - Class in etomica.normalmode
-
- SimLJVacancy.LJParams - Class in etomica.normalmode
-
- SimModesJ - Class in etomica.normalmode
-
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.
- SimModesJ(Space, int) - Constructor for class etomica.normalmode.SimModesJ
-
- SimOverlap - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlap(Space, int, double, double, String, double) - Constructor for class etomica.normalmode.SimOverlap
-
- SimOverlap.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapAlphaN2TP - Class in etomica.models.nitrogen
-
Temperature-perturbation simulation for alpha-phase Nitrogen
- SimOverlapAlphaN2TP(Space, int[], double, double, double[], double[], int, double, long, double, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- SimOverlapAlphaN2TP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapBetaN2RP - Class in etomica.models.nitrogen
-
- SimOverlapBetaN2RP(Space, int, double, double, double[], double, double, int) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- SimOverlapBetaN2RP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
- SimOverlapBetaN2RPScaling - Class in etomica.models.nitrogen
-
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
- SimOverlapBetaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- SimOverlapBetaN2RPScaling.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapBetaN2TP - Class in etomica.models.nitrogen
-
Temperature-perturbation simulation for beta-phase Nitrogen
- SimOverlapBetaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- SimOverlapBetaN2TP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapDisorderedAlphaN2RPScaling - Class in etomica.models.nitrogen
-
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
- SimOverlapDisorderedAlphaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapDisorderedAlphaN2TP - Class in etomica.models.nitrogen
-
Temperature-perturbation simulation for disordered alpha-phase Nitrogen
- SimOverlapDisorderedAlphaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- SimOverlapDisorderedAlphaN2TP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapLJ - Class in etomica.normalmode
-
Simulation to run sampling with the LJ potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapLJ(Space, int, double, double, double) - Constructor for class etomica.normalmode.SimOverlapLJ
-
- SimOverlapLJ.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapLJModule - Class in etomica.normalmode
-
Main method that constructs an overlap sampling module to calculate the free
energy difference between a harmonic system and a lennard jones solid.
- SimOverlapLJModule() - Constructor for class etomica.normalmode.SimOverlapLJModule
-
- SimOverlapLJModule.APIPotentialReference - Class in etomica.normalmode
-
- SimOverlapLJModule.APIPotentialTarget - Class in etomica.normalmode
-
- SimOverlapLJModule.MeterPotentialEnergyDifference - Class in etomica.normalmode
-
- SimOverlapLJModule.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapModule - Class in etomica.normalmode
-
Overlap sampling "module" to calculate free energy difference.
- SimOverlapModule(IBox, IBox, IIntegrator, IIntegrator, IAPIPotential, IAPIPotential, double) - Constructor for class etomica.normalmode.SimOverlapModule
-
- SimOverlapMultiHarmonic - Class in etomica.gaussianwork
-
MultiHarmonic Overlap Simulation
a.
- SimOverlapMultiHarmonic(int, double, double, double) - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- SimOverlapMultiHarmonic.SimOverlapParam - Class in etomica.gaussianwork
-
- SimOverlapMultiHarmonicOptRefPref - Class in etomica.gaussianwork
-
MultiHarmonic Overlap Simulation
a.
- SimOverlapMultiHarmonicOptRefPref(int, double, double, double, double) - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- SimOverlapMultiHarmonicOptRefPref.SimOverlapParam - Class in etomica.gaussianwork
-
- SimOverlapMultipleWaveVectors - Class in etomica.models.oneDHardRods
-
- SimOverlapMultipleWaveVectors(Space, int, double, double, String, double, int[], int[]) - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam - Class in etomica.models.oneDHardRods
-
- SimOverlapMultipleWaveVectorsParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- SimOverlapMultipleWaveVectorsParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- SimOverlapMultipleWV3DLJ - Class in etomica.models.oneDHardRods
-
- SimOverlapMultipleWV3DLJ(Space, int, double, double, String, double, int[], int[]) - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam - Class in etomica.models.oneDHardRods
-
- SimOverlapNitrogenModel - Class in etomica.models.nitrogen
-
Simulation to run sampling with the nitrogen model to find the free energy difference
between the harmonic reference system and the target system
The Bennett's Overlapping Sampling Simulation
- used to check for the computation time
- SimOverlapNitrogenModel(Space, int, double, String, double) - Constructor for class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- SimOverlapNitrogenModel.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapParam() - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlap.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- SimOverlapSoftSphere - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphere(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphere
-
- SimOverlapSoftSphere.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereDP - Class in etomica.normalmode
-
Simulation to run density perturbation for soft spheres.
- SimOverlapSoftSphereDP(Space, int, boolean, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereDP
-
- SimOverlapSoftSphereDP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereEin - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimOverlapSoftSphereEin(Space, int, double, boolean, double, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin
-
- SimOverlapSoftSphereEin.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimOverlapSoftSphereEin.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereEinHarm - Class in etomica.normalmode
-
Overlap sampling simulation whose target system has a composite energy
function (soft sphere and Einstein crystal) and whose reference system is
defined by (harmonically coupled) normal modes and Einstein crystal.
- SimOverlapSoftSphereEinHarm(Space, int, double, boolean, double, double, double, int, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimOverlapSoftSphereEinHarm.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereHCP - Class in etomica.normalmode
-
Simulation to run sampling with the soft-sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereHCP(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereHCP
-
- SimOverlapSoftSphereHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereReweighting - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereReweighting(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- SimOverlapSoftSphereReweighting.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereSoftness - Class in etomica.normalmode
-
Conduct Bennett's Overlap Sampling to quantify the free-energy difference
between soft-sphere model with different softness
Soft-Sphere potential: U = epsilon*(sigma/r)^n
where n is the exponent, s = 1/n (where s is softness)
epsilon and sigma is set to 1
- SimOverlapSoftSphereSoftness(Space, int, double, double, double, int[], double, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- SimOverlapSoftSphereSoftness.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereSuperBox - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereSuperBox(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- SimOverlapSoftSphereSuperBox.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereTP - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereTP(Space, int, boolean, boolean, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTP
-
- SimOverlapSoftSphereTP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereTPHCP - Class in etomica.normalmode
-
The original Bennett's Overlapping Sampling Simulation
- used to check for the computation time
- SimOverlapSoftSphereTPHCP(Space, int, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- SimOverlapSoftSphereTPHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereTPSlantedBox - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereTPSlantedBox(Space, int, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- SimOverlapSoftSphereTPSlantedBox.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSsNxy - Class in etomica.models.oneDHardRods
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSsNxy(Space, int, double, double, String, double, int, int[], double) - Constructor for class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- SimOverlapSSnxy - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSSnxy(Space, int, double, double, String, double, int, int[]) - Constructor for class etomica.normalmode.SimOverlapSSnxy
-
- SimOverlapSsNxy.SimOverlapParam - Class in etomica.models.oneDHardRods
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSSnxy.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapTPSSParams() - Constructor for class etomica.normalmode.HTTPSoftSphereApplet.SimOverlapTPSSParams
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- SimParams() - Constructor for class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- SimParams() - Constructor for class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestHSMD3D.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestLJMC3D.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestSWChain.SimParams
-
- Simple() - Constructor for class etomica.graphics.ColorScheme.Simple
-
- Simple(Color) - Constructor for class etomica.graphics.ColorScheme.Simple
-
- SimpleElementForSimilarSpecies - Class in etomica.virial.GUI.components
-
- simpleReplace(String, String, String) - Static method in class org.jmol.util.TextFormat
-
Does a clean replace of strFrom in str with strTo
If strTo contains strFrom, then only a single pass is done.
- SimpleUnit - Class in etomica.units
-
Superclass for all base unit classes.
- SimpleUnit(Dimension, double, String, String, boolean) - Constructor for class etomica.units.SimpleUnit
-
Constructor.
- simplifiedP3NonAdd - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- simplifiedP3NonAdd - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- simplify() - Method in class etomica.util.Rational
-
Simplify the rational.
- simplify() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Simplify the representation.
- simRealT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simRealT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimTarget - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimTarget(Space, int, double) - Constructor for class etomica.normalmode.SimTarget
-
- SimTargetUmbrella - Class in etomica.normalmode
-
Simulation to sample target system and perturbing into
the umbrella sampling region
- SimTargetUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimTargetUmbrella
-
- SimTargetUmbrella.SimBennetParam - Class in etomica.normalmode
-
- simType - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- simType - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- simulation - Variable in class etomica.action.SimulationActionAdapter
-
- simulation - Variable in class etomica.graphics.SimulationGraphic
-
- simulation - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- simulation - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- simulation - Variable in class etomica.nbr.PotentialMasterNbr
-
- Simulation - Class in etomica.simulation
-
The main class that organizes the elements of a molecular simulation.
- Simulation(ISpace) - Constructor for class etomica.simulation.Simulation
-
Creates a new simulation using the given space
- SimulationAction - Interface in etomica.action
-
Interface for classes that apply some elementary action (transformation) to a
simulation.
- SimulationActionAdapter - Class in etomica.action
-
Convenience class used to define a SimulationAction.
- SimulationActionAdapter() - Constructor for class etomica.action.SimulationActionAdapter
-
- SimulationAlphaNitrogenModel - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
alpha-N2 crystal Structure
- SimulationAlphaNitrogenModel(ISpace, int[], double, double) - Constructor for class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- SimulationAtomTypeEvent - Class in etomica.simulation
-
- SimulationAtomTypeEvent(ISimulation, IAtomType) - Constructor for class etomica.simulation.SimulationAtomTypeEvent
-
- simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationAtomTypeIndexEvent - Class in etomica.simulation
-
- SimulationAtomTypeIndexEvent(ISimulation, IAtomType, int) - Constructor for class etomica.simulation.SimulationAtomTypeIndexEvent
-
- simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationBetaNitrogenModel - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
beta-N2 crystal Structure
- SimulationBetaNitrogenModel(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- SimulationBetaNitrogenModelTest - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
beta-N2 crystal Structure
- SimulationBetaNitrogenModelTest(ISpace, int[], double, double, double) - Constructor for class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- simulationBoxAdded(ISimulationBoxEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationBoxEvent - Class in etomica.simulation
-
- SimulationBoxEvent(ISimulation, IBox) - Constructor for class etomica.simulation.SimulationBoxEvent
-
- simulationBoxRemoved(ISimulationBoxEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationContainer - Interface in etomica.simulation
-
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
- SimulationDataAction - Class in etomica.action
-
Action that performs a call to the reset() method of a set
of accumulators, as specified via a list of AccumulatorManager
instances.
- SimulationDataAction(DataStreamAction) - Constructor for class etomica.action.SimulationDataAction
-
- SimulationEvent - Class in etomica.simulation
-
- SimulationEvent(ISimulation) - Constructor for class etomica.simulation.SimulationEvent
-
- SimulationEventManager - Class in etomica.simulation
-
- SimulationEventManager(ISimulation) - Constructor for class etomica.simulation.SimulationEventManager
-
- SimulationGammaNitrogenModel - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
gamma-N2 crystal Structure
- SimulationGammaNitrogenModel(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- SimulationGraphic - Class in etomica.graphics
-
General class for graphical presentation of the elements of a molecular simulation.
- SimulationGraphic(ISimulation, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(ISimulation, int, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(ISimulation, String, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(ISimulation, int, String, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(ISimulation, String, int, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(ISimulation, int, String, int, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationIndexEvent - Class in etomica.simulation
-
- SimulationIndexEvent(ISimulation, int) - Constructor for class etomica.simulation.SimulationIndexEvent
-
- SimulationOrthorhombicParacetamol - Class in etomica.paracetamol
-
Simulation of 3D Paracetamol molecules in Form II (Orthorhombic)
- SimulationOrthorhombicParacetamol(Space, int, double) - Constructor for class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- SimulationPanel - Class in etomica.graphics
-
Main panel used to display the graphical elements of a simulation.
- SimulationPanel() - Constructor for class etomica.graphics.SimulationPanel
-
- SimulationPanel(String) - Constructor for class etomica.graphics.SimulationPanel
-
- SimulationRestart - Class in etomica.action
-
Action that invokes reset method of all registered simulation elements,
effectively initializing the entire simulation.
- SimulationRestart(ISimulation, ISpace, IController) - Constructor for class etomica.action.SimulationRestart
-
- SimulationRheology - Class in etomica.modules.rheology
-
Simulation for rheology module.
- SimulationRheology(ISpace) - Constructor for class etomica.modules.rheology.SimulationRheology
-
- SimulationRunner - Class in etomica.virial.GUI.components
-
- SimulationRunner(ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.components.SimulationRunner
-
- simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationSpeciesEvent - Class in etomica.simulation
-
- SimulationSpeciesEvent(ISimulation, ISpecies) - Constructor for class etomica.simulation.SimulationSpeciesEvent
-
- simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationSpeciesIndexEvent - Class in etomica.simulation
-
- SimulationSpeciesIndexEvent(ISimulation, ISpecies, int) - Constructor for class etomica.simulation.SimulationSpeciesIndexEvent
-
- simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.box.BoxAgentManager
-
- simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in interface etomica.api.ISimulationListener
-
- simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.atom.MoleculeAgentManager
-
- simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.atom.SpeciesAgentManager
-
- simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.box.BoxAgentManager
-
- SimulationVirial - Class in etomica.virial.simulations
-
Generic simulation using Mayer sampling to evaluate cluster integrals
- SimulationVirial(ISpace, ISpecies[], int[], double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(ISpace, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
Constructor for simulation to determine the ratio between reference and target Clusters
- SimulationVirial(ISpace, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(ISpace, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(ISpace, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(ISpace, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirialDiagram - Class in etomica.virial.simulations
-
Virial simulation using diagram sampling.
- SimulationVirialDiagram(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialDiagram
-
- SimulationVirialMultiOverlap - Class in etomica.virial.simulations
-
- SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract, ClusterAbstract, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract, ClusterAbstract, boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract[], ClusterWeight[], boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- SimulationVirialOverlap - Class in etomica.virial.simulations
-
- SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract, boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap(Space, SpeciesFactory[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap2 - Class in etomica.virial.simulations
-
Simulation implementing the overlap-sampling approach to evaluating a cluster
diagram.
- SimulationVirialOverlap2(ISpace, ISpecies, int, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
This constructor will create your simulation class, but you may call
set methods before using it.
- SimulationVirialOverlap2(ISpace, ISpecies[], int[], double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
This constructor will create your simulation class, but you may call
set methods before using it.
- SimulationVirialOverlap2(ISpace, ISpecies, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(ISpace, ISpecies, double, ClusterAbstract, ClusterAbstract, boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(ISpace, ISpecies, double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(ISpace, ISpecies[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(ISpace, ISpecies[], int[], double, ClusterAbstract[], ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2.BoxClusterFactory - Class in etomica.virial.simulations
-
- SimulationVirialPT - Class in etomica.virial.simulations
-
Generic simulation using Mayer sampling to evaluate cluster integrals
- SimulationVirialPT(Space, SpeciesFactory, double[], ClusterWeight.Factory, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialPT
-
Constructor for simulation to determine the ratio bewteen reference and target Clusters
- SimulationVirialUmbrella - Class in etomica.virial.simulations
-
Simulation implementing the umbrella-sampling approach to evaluating a cluster
diagram.
- SimulationVirialUmbrella(Space, double, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialUmbrella
-
- SimulationVirialUmbrella(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialUmbrella
-
- SimulationWorker(int, int, int, MayerFunction, MayerFunction, int, double, double, double, long, ISpace, String, double, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean) - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- SimulationWorker(int, int, MayerFunction, MayerFunction, MayerFunction, double, double, double, double, long, ISpace, String, double, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean) - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- SimUmbrella - Class in etomica.normalmode
-
Simulation to sample Umbrella Sampling
- SimUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimUmbrella
-
- SimUmbrella.SimBennetParam - Class in etomica.normalmode
-
- SimUmbrellaSoftSphere - Class in etomica.normalmode
-
Simulation to sample Umbrella Overlap Sampling
The original Umbrella Sampling Simulation
- used to check for the computation time
- SimUmbrellaSoftSphere(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimUmbrellaSoftSphere
-
- SimUmbrellaSoftSphere.SimBennetParam - Class in etomica.normalmode
-
- simWaveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simWaveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimWidomMode - Class in etomica.models.oneDHardRods
-
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
- SimWidomMode(Space, int, double, int) - Constructor for class etomica.models.oneDHardRods.SimWidomMode
-
- SimWidomMode.SimParam - Class in etomica.models.oneDHardRods
-
- simWVCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simWVCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- sin() - Method in class etomica.math.Complex
-
Sine of this Complex number (doesn't change this Complex number).
- sin(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Trigonometric sine.
- sinDtheta - Variable in class etomica.dimer.IntegratorDimerMin
-
- SineTransform - Class in etomica.util
-
3D Fourier transforms of a function, f, simplify to 1D sine transforms of the auxiliary function F(r) = r*f(r)
when f is spherically symmetric.
- SineTransform() - Constructor for class etomica.util.SineTransform
-
- sinGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
-
- sinGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- singleAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- singleAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- singleAction - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- singleAction - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- SingleAssociationSiteFluid - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid
-
- SingleAssociationSiteFluid.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid2 - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
- SingleAssociationSiteFluid2() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2
-
- SingleAssociationSiteFluid2.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid2Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
2points and 3 points diagram calculation
- SingleAssociationSiteFluid2Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2Pt
-
- SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid3Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
2points and 3 points diagram calculation
- SingleAssociationSiteFluid3Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid3Pt
-
- SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid4Points - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid4Points() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Points
-
- SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid4Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's double attraction-site model
4points diagram calculation
- SingleAssociationSiteFluid4Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Pt
-
- SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluidGraph - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
- SingleAssociationSiteFluidGraph() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluidGraph
-
- SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleDipole - Class in etomica.rotation
-
- SingleDipole() - Constructor for class etomica.rotation.SingleDipole
-
- SingleDipole.Applet - Class in etomica.rotation
-
- SingleDumbellRattle - Class in etomica.rotation
-
- SingleDumbellRattle() - Constructor for class etomica.rotation.SingleDumbellRattle
-
- SingleDumbellRattle.Applet - Class in etomica.rotation
-
- SingleDumbellShake - Class in etomica.rotation
-
- SingleDumbellShake() - Constructor for class etomica.rotation.SingleDumbellShake
-
- SingleDumbellShake.Applet - Class in etomica.rotation
-
- singlet - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- singlet - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- singletId(int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
- SingleValueOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
-
- SingleWater - Class in etomica.rotation
-
- SingleWater() - Constructor for class etomica.rotation.SingleWater
-
- SingleWater.Applet - Class in etomica.rotation
-
- SingleWaterMatrix - Class in etomica.rotation
-
- SingleWaterMatrix() - Constructor for class etomica.rotation.SingleWaterMatrix
-
- SingleWaterMatrix.Applet - Class in etomica.rotation
-
- SingleWaterRattle - Class in etomica.rotation
-
- SingleWaterRattle() - Constructor for class etomica.rotation.SingleWaterRattle
-
- SingleWaterRattle.Applet - Class in etomica.rotation
-
- SingleWaterShake - Class in etomica.rotation
-
- SingleWaterShake() - Constructor for class etomica.rotation.SingleWaterShake
-
- SingleWaterShake.Applet - Class in etomica.rotation
-
- sinh() - Method in class etomica.math.Complex
-
Hyperbolic sine of this Complex number
(doesn't change this Complex number).
- sinh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The hyperbolic sine.
- sink - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- sink - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- sink0 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- sink0 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkDy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- sinkDy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- sinkDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkDy3 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkEigen - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- sinkEy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- sinkEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkrj - Variable in class etomica.potential.EwaldSummation
-
- sinkSmoothed - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
-
- sinkSmoothed - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkTrue - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkTrueEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
-
- sinkWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- sinTheta - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- sinTheta - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- sinusoidalB - Variable in class etomica.modules.sam.Sam
-
- site(int[]) - Method in class etomica.config.ConfigurationLattice.MyLattice
-
Returns the same instance of IVector with each call.
- site(int[]) - Method in interface etomica.lattice.AbstractLattice
-
Returns the site specified by the given index.
- site(int[]) - Method in class etomica.lattice.BravaisLattice
-
Calculates and returns a vector that is the spatial position given
by adding together the primitive vectors, each multiplied by the corresponding
integer index given by the array argument.
- site(int[]) - Method in class etomica.lattice.BravaisLatticeCrystal
-
Returns a Vector instance giving the location of the referenced site.
- site(IVector) - Method in class etomica.lattice.CellLattice
-
Returns the cell in which the given point lies.
- site(int[]) - Method in class etomica.lattice.RectangularLattice
-
Returns the instance of the object associated with the given index.
- site(int[]) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
-
Returns the same instance of IVector with each call.
- site(int[]) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
-
Returns the same instance of IVector with each call.
- site - Static variable in class org.jmol.script.Token
-
- siteat - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- sitebt - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- siteDisplacement - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- siteDisplacement - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- siteDoubles - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- siteFactor - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- siteFactory - Variable in class etomica.lattice.RectangularLattice
-
- SiteFactory - Interface in etomica.lattice
-
Interface for a class that generates the sites populating a lattice.
- siteID - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- siteID - Static variable in class etomica.potential.P2NitrogenHellmann
-
- siteID - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- SiteIterator - Interface in etomica.lattice
-
Interface for objects that iterate over some or all of the
sites of a lattice.
- siteManager - Variable in class etomica.normalmode.CoordinateDefinition
-
- sitePos - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- sitePos - Variable in class etomica.models.water.P2WaterSzalewicz
-
- sitePos3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- sitePosA - Static variable in class etomica.potential.P2NitrogenHellmann
-
- sitePosA - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- sitePosB - Static variable in class etomica.potential.P2NitrogenHellmann
-
- sitePosB - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- sites() - Method in interface etomica.lattice.FiniteLattice
-
Returns an array containing all the sites in the lattice.
- sites - Variable in class etomica.lattice.RectangularLattice
-
- sites() - Method in class etomica.lattice.RectangularLattice
-
- sites - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- sitesCO2L - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- sitesHH - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- sitesOH - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- SiteSource(ISpace) - Constructor for class etomica.normalmode.CoordinateDefinition.SiteSource
-
- sixId(int, int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5)
and given number of molecules (n).
- sixId(int, int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5)
and given number of molecules (n).
- sixStart - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- sixStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
-
- size() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- size() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- size() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- size() - Method in class etomica.atom.iterator.ApiIndexList
-
- size() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.ApiIntergroup
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiIntergroupCoupled
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.ApiIntragroup
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
- size() - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Returns the number of iterates that iterator would give
if reset and iterated in its current condition.
- size() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
-
- size() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
-
- size() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
-
- size() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- size() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
returns 1 if atom is not null, 0 if atom is null.
- size() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- size() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- size() - Method in interface etomica.atom.iterator.AtomsetIterator
-
The number of iterates returned by this iterator in its current state.
- size() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
- size() - Method in class etomica.atom.iterator.MoleculeIteratorAll
-
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
- size() - Method in class etomica.atom.iterator.MoleculeIteratorArrayList
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet
-
returns 1 if atom is not null, 0 if atom is null.
- size() - Method in class etomica.atom.iterator.MpiInnerFixed
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.MpiInnerVariable
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.MpiInterArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.MpiInterspecies1A
-
- size() - Method in class etomica.atom.iterator.MpiInterspeciesAA
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.MpiIntraArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.MpiIntraspecies1A
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.atom.iterator.MpiIntraspeciesAA
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.MpiMolecule
-
Returns the number of iterates that would be given
when iterating after reset.
- size() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- size() - Method in class etomica.graph.model.GraphList
-
- size() - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- size() - Method in class etomica.graph.operations.RelabelParameters
-
- size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- size - Variable in class etomica.lattice.crystal.Primitive
-
- size() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- size - Variable in class etomica.lattice.RectangularLattice
-
- size() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
The number of iterates returned by this iterator in its current state.
- size() - Method in interface etomica.lattice.SiteIterator
-
Returns the number of iterates that this iterator would give
if reset.
- size - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- size - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- size - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- size() - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder
-
- size() - Method in class etomica.nbr.cell.Api1ACell
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.nbr.cell.ApiAACell
-
Returns the number of atom pairs the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.cell.AtomIteratorCell
-
Returns the number of atoms the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
Returns the number of atoms the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
Returns the number of atom pairs the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.site.Api1ASite
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- size() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- size() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- size() - Method in class etomica.util.ObjectArrayList
-
Returns the number of elements in this list.
- size() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Count of coefficients.
- size() - Method in class org.jmol.util.BitSet
-
Returns the number of bits of space actually in use by this BitSet
to represent bit values.
- SIZE_INCREASE_RATIO - Static variable in class etomica.atom.AtomArrayList
-
- SIZE_INCREASE_RATIO - Static variable in class etomica.atom.MoleculeArrayList
-
- sizeCellX - Variable in class etomica.modules.sam.Sam
-
- sizeCellZ - Variable in class etomica.modules.sam.Sam
-
- sizeOf(Token) - Static method in class org.jmol.script.ScriptVariable
-
- sizeOfArray() - Method in class etomica.atom.AtomArrayList
-
- sizeOfArray() - Method in class etomica.atom.MoleculeArrayList
-
- sizePanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- skew - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- SKEW - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- SKEW - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- slab - Static variable in class org.jmol.script.Token
-
- slab - Variable in class org.jmol.util.GData
-
- slabBrillouin(Point3f[]) - Method in class org.jmol.util.MeshSurface
-
- slabbyatom - Static variable in class org.jmol.script.Token
-
- slabbymolecule - Static variable in class org.jmol.script.Token
-
- slabColix - Variable in class org.jmol.util.MeshSurface
-
- slabenabled - Static variable in class org.jmol.script.Token
-
- slabMeshType - Variable in class org.jmol.util.MeshSurface
-
- slabOptions - Variable in class org.jmol.util.MeshSurface
-
- slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSurface
-
- slabPolygonsList(List<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
-
- slabrange - Static variable in class org.jmol.script.Token
-
- slabValue - Variable in class g3dsys.control.TransformManager
-
- slanty - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- slider - Variable in class etomica.graphics.DeviceSlider
-
Subclass of Swing slider displayed to screen
located in utility package
- sliderA - Variable in class etomica.modules.rheology.RheologyGraphic
-
- sliders(int, int, String, P2SquareWellBonded) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
-
- sliders(int, int, String, P2SquareWellBonded) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- sliders(int, int, String, P2SquareWellRadical[]) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- smallmoleculemaxatoms - Static variable in class org.jmol.script.Token
-
- smartaromatic - Static variable in class org.jmol.script.Token
-
- smerList - Variable in class etomica.association.ColorSchemeSmer.ColorAgent
-
- smerList - Variable in class etomica.association.ColorSchemeSmer
-
- smerList - Variable in class etomica.association.ColorSchemeSmerByLength
-
- smerList - Variable in class etomica.association.MCMoveAtomMonomer
-
- smerList - Variable in class etomica.association.MCMoveAtomSmer
-
- smerList - Variable in class etomica.association.MCMoveBiasUB
-
- smerList - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- smerList - Variable in class etomica.association.MCMoveMoleculeMonomer
-
- smerList - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
-
- smerList - Variable in class etomica.association.MCMoveMoleculeSmer
-
- smerList - Variable in class etomica.association.MCMoveRotateAssociated
-
- smerList - Variable in class etomica.association.MCMoveSmer
-
- smerList - Variable in class etomica.association.MCMoveSmerRotate
-
- smerList - Variable in class etomica.association.MCMoveVolumeAssociated
-
- smerList - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- smiles2dimageformat - Static variable in class org.jmol.script.Token
-
- smilesurlformat - Static variable in class org.jmol.script.Token
-
- sn - Variable in class etomica.dimer.EnergyMap
-
- sn - Variable in class etomica.meam.MEAM_MC
-
- sn - Variable in class etomica.meam.MEAMMd3D
-
- Sn - Static variable in class etomica.meam.ParameterSetMEAM
-
- sn - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- snA - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- snA - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- snA - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- snAdatom - Variable in class etomica.dimer.EnergyMap
-
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
-
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
-
- snapshotTime - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Document time to seek to.
- snB - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- snFix - Variable in class etomica.dimer.EnergyMap
-
- snFixedA - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- snFixedA - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- snFixedA - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- snFixedB - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- so2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- Sodium - Class in etomica.chem.elements
-
Class for the Sodium element.
- Sodium(String) - Constructor for class etomica.chem.elements.Sodium
-
- Sodium(String, double) - Constructor for class etomica.chem.elements.Sodium
-
- SoftSphere3d - Class in etomica.simulation.prototypes
-
Simple hard-sphere Monte Carlo simulation in 2D.
- SoftSphere3d(double, int, double) - Constructor for class etomica.simulation.prototypes.SoftSphere3d
-
- SoftSphereSolidEOS - Class in etomica.normalmode
-
Soft-Sphere Solid Equation of State
for n = 12, 9 and 6
Reference: Tan, Schultz and Kofke, J Chem.
- SoftSphereSolidEOS() - Constructor for class etomica.normalmode.SoftSphereSolidEOS
-
- SoftSphereSolidEOSCalculator - Class in etomica.normalmode
-
- SoftSphereSolidEOSCalculator() - Constructor for class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- soluteChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- soluteChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- soluteChargeSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- soluteMoleFraction - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- soluteMoleFraction - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- soluteMoleFractionSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- soluteMoleFractionSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- solutionChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- solutionChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- solve(Matrix) - Method in class etomica.math.linearalgebra.Matrix
-
- solve(BigInteger[][], BigInteger[]) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Solve a linear system of equations.
- solveCoefficients() - Method in class etomica.util.numerical.PadeApproximation
-
- solvent - Static variable in class org.jmol.script.Token
-
- solventChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- solventChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- solventChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- solventChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- solventprobe - Static variable in class org.jmol.script.Token
-
- solventproberadius - Static variable in class org.jmol.script.Token
-
- solventThermoFrac - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- sort() - Method in class etomica.graph.model.GraphList
-
- sort(int[], int) - Method in class etomica.graph.property.FactorFFT
-
- sort() - Method in class etomica.virial.cluster.ClusterDiagram
-
Sorts list of connections for each node in the diagram such that
mConnections[i][j] < mConnections[i][k] for k > j.
- sort - Static variable in class org.jmol.g3d.Graphics3D
-
- Sort(int) - Constructor for class org.jmol.script.ScriptVariable.Sort
-
- sortConnections(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
- sortDiagrams(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Sorts diagrams in order from most bonds to fewest bonds
- sorted - Variable in class etomica.graph.model.GraphList
-
- sortedItem(List<String>, int) - Static method in class org.jmol.util.ArrayUtil
-
- sortKey - Variable in class etomica.util.TreeLinker
-
- sortOrReverse(int) - Method in class org.jmol.script.ScriptVariable
-
- source - Variable in class etomica.integrator.IntegratorEvent
-
- sources - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Sources files or URLs
- SOUTH - Static variable in class etomica.util.Constants.CompassDirection
-
- space - Variable in class etomica.action.SimulationActionAdapter
-
- space - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- space - Variable in class etomica.AlkaneEH.ConformationMethane
-
- space - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- space - Variable in class etomica.AlkaneEH.SpeciesMethane
-
- space - Variable in class etomica.association.BiasVolume
-
- space - Variable in class etomica.association.BiasVolumeMolecule
-
- space - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- space - Variable in class etomica.association.MCMoveDimer
-
- space - Variable in class etomica.association.MCMoveDimerRotate
-
- space - Variable in class etomica.association.MCMoveSmer
-
- space - Variable in class etomica.association.MCMoveSmerRotate
-
- space - Variable in class etomica.config.ConfigurationLattice
-
- space - Variable in class etomica.config.ConformationChain
-
- space - Variable in class etomica.config.ConformationChainLinear
-
- space - Variable in class etomica.config.ConformationLinear
-
- space - Variable in class etomica.config.ConformationWater
-
- space - Variable in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
-
- space - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
-
- space - Variable in class etomica.data.DataProcessorInterfacialTension
-
- space - Variable in class etomica.data.DataSourceAtomDistance
-
- space - Variable in class etomica.data.meter.MeterDihedralAngle
-
- space - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- space - Variable in class etomica.data.meter.MeterRDF
-
- space - Variable in class etomica.data.meter.MeterRDFPC
-
- space - Variable in class etomica.data.meter.MeterStructureFactor
-
- space - Variable in class etomica.data.types.DataTensor.DataInfoTensor
-
- space - Variable in class etomica.data.types.DataTensor.DataInfoTensorFactory
-
- space - Variable in class etomica.data.types.DataVector.DataInfoVector
-
- space - Variable in class etomica.data.types.DataVector.DataInfoVectorFactory
-
- space - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- space - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- space - Variable in class etomica.graphics.DisplayBoxCanvas2D
-
- space - Variable in class etomica.graphics.SimulationGraphic
-
- space - Variable in class etomica.integrator.IntegratorMD
-
- space - Variable in class etomica.integrator.IntegratorMD.VectorSource
-
- space - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- space - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- space - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- space - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- space - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- space - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- space - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- space - Variable in class etomica.interfacial.ConfigurationLammps
-
- space - Variable in class etomica.interfacial.MeterWallForce
-
- space - Variable in class etomica.lattice.crystal.Primitive
-
- space - Variable in class etomica.mappedvirial.MappedUpotential
-
- space - Variable in class etomica.mappedvirial.MeterMappedU
-
- space - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- space - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- space - Variable in class etomica.mappedvirial.MeterMeanForce
-
- space - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- space - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- space - Static variable in class etomica.math.Quaternion
-
- space - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- space - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- space - Variable in class etomica.models.co2.P2CO2Hellmann
-
- space - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- space - Variable in class etomica.models.nitrogen.ConformationNitrogen
-
- space - Variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- space - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- space - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- space - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- space - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- space - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- space - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.SpeciesN2
-
- space - Variable in class etomica.models.nitrogen.SpeciesN2B
-
- space - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- space - Variable in class etomica.models.nitrogen.TestRotationVector
-
- space - Variable in class etomica.models.OPLS.ConformationAceticAcid
-
- space - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- space - Variable in class etomica.models.rowley.ConformationEthanol
-
- space - Variable in class etomica.models.rowley.ConformationMethanol
-
- space - Variable in class etomica.models.rowley.SpeciesEthanol
-
- space - Variable in class etomica.models.rowley.SpeciesMethanol
-
- space - Variable in class etomica.models.traPPE.ConformationMethanol
-
- space - Variable in class etomica.models.traPPE.SpeciesMethanol
-
- space - Variable in class etomica.models.water.ConfigurationFileTIP4P
-
- space - Variable in class etomica.models.water.ConformationWater3P
-
- space - Variable in class etomica.models.water.ConformationWaterGCPM
-
- space - Variable in class etomica.models.water.ConformationWaterTIP4P
-
- space - Variable in class etomica.models.water.P2WaterSzalewicz
-
- space - Variable in class etomica.models.water.SpeciesWater3P
-
- space - Variable in class etomica.models.water.SpeciesWater3POriented
-
- space - Variable in class etomica.models.water.SpeciesWater4P
-
- space - Variable in class etomica.models.water.SpeciesWater4PCOM
-
- space - Variable in class etomica.models.water.SpeciesWater4POriented
-
- space - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- space - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- space - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- space - Variable in class etomica.modules.dcvgcmd.ConformationTube
-
- space - Variable in class etomica.modules.materialfracture.P1Tension
-
- space - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- space - Variable in class etomica.modules.sam.ConfigurationSAM
-
- space - Variable in class etomica.modules.sam.P1Sinusoidal
-
- space - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- space - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- space - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- space - Variable in class etomica.nbr.CriterionSimple
-
- space - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- space - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- space - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- space - Variable in class etomica.nbr.list.PotentialMasterList
-
- space - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- space - Variable in class etomica.normalmode.ConformationHSDimer
-
- space - Variable in class etomica.normalmode.CoordinateDefinition
-
- space - Variable in class etomica.normalmode.HSNPT.ActionSummer
-
- space - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- space - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- space - Variable in class etomica.normalmode.MCMoveWV
-
- space - Variable in class etomica.normalmode.MeterDADB
-
- space - Variable in class etomica.normalmode.MeterSolidProps
-
- space - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- space - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- space - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- space - Variable in class etomica.normalmode.NormalModes2D
-
- space - Variable in class etomica.normalmode.NormalModes3D
-
- space - Variable in class etomica.normalmode.NormalModesMolecular
-
- space - Variable in class etomica.normalmode.NormalModesPotential
-
- space - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- space - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- space - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- space - Variable in class etomica.normalmode.SpeciesHSDimer
-
- space - Variable in class etomica.normalmode.WaveVectorFactorySimple
-
- space - Variable in class etomica.paracetamol.ConformationParacetamol
-
- space - Variable in class etomica.paracetamol.ConformationParacetamolMonoclinic
-
- space - Variable in class etomica.paracetamol.ConformationParacetamolOrthorhombic
-
- space - Variable in class etomica.paracetamol.SpeciesParacetamol
-
- space - Variable in class etomica.parser.ParserLAMMPS.Options
-
- space - Variable in class etomica.potential.EwaldSummation
-
- space - Variable in class etomica.potential.EwaldSumMolecules
-
- space - Variable in class etomica.potential.P2HardWrapper
-
- space - Variable in class etomica.potential.P2NitrogenHellmann
-
- space - Variable in class etomica.potential.P2O2Bartolomei
-
- space - Variable in class etomica.potential.P2SemiclassicalAtomic
-
- space - Variable in class etomica.potential.P2SemiclassicalMolecular
-
- space - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- space - Variable in class etomica.potential.P3AxilrodTeller
-
- space - Variable in class etomica.potential.P3Induction
-
- space - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- space - Variable in class etomica.potential.Potential
-
- space - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- space - Variable in class etomica.potential.PotentialMolecular
-
- space - Variable in class etomica.simulation.Simulation
-
- space - Variable in class etomica.space.Boundary
-
- Space - Class in etomica.space
-
- Space() - Constructor for class etomica.space.Space
-
- space - Variable in class etomica.species.SpeciesOriented
-
- space - Variable in class etomica.species.SpeciesSpheres
-
- space - Variable in class etomica.species.SpeciesSpheresCustom
-
- space - Variable in class etomica.species.SpeciesSpheresHetero
-
- space - Variable in class etomica.species.SpeciesSpheresMono
-
- space - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- space - Variable in class etomica.virial.BoxCluster
-
- space - Variable in class etomica.virial.ClusterCoupledFlipped
-
- space - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- space - Variable in class etomica.virial.ConfigurationCluster
-
- space - Variable in class etomica.virial.Conformation7SiteRigidSF6
-
- space - Variable in class etomica.virial.ConformationAlkaneEH
-
- space - Variable in class etomica.virial.ConformationAnthracene3site
-
- space - Variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- space - Variable in class etomica.virial.ConformationCO2
-
- space - Variable in class etomica.virial.ConformationMethane
-
- space - Variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- space - Variable in class etomica.virial.ConformationPh3site
-
- space - Variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- space - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- space - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- space - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- space - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- space - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- space - Variable in class etomica.virial.MCMoveClusterRingScale
-
- space - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- space - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- space - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- space - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- space - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- space - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- space - Variable in class etomica.virial.Species7SiteRigidSF6
-
- space - Variable in class etomica.virial.SpeciesAlkaneEH
-
- space - Variable in class etomica.virial.SpeciesAnthracene3site464
-
- space - Variable in class etomica.virial.SpeciesAnthracene3site545
-
- space - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- space - Variable in class etomica.virial.SpeciesFactorySpheres2
-
- space - Variable in class etomica.virial.SpeciesMethane
-
- space - Variable in class etomica.virial.SpeciesPh3site464
-
- space - Variable in class etomica.virial.SpeciesPh3site545
-
- space - Variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- space - Variable in class etomica.virial.SpeciesTraPPECO2
-
- space - Variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- space - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- Space1D - Class in etomica.space1d
-
Factory and methods appropriate to a 1-dimensional space.
- Space2D - Class in etomica.space2d
-
Factory and methods appropriate to a 2-dimensional space.
- Space3D - Class in etomica.space3d
-
Factory and methods appropriate to a 3-dimensional space.
- spacefill - Static variable in class org.jmol.script.Token
-
- SpaceLattice - Interface in etomica.lattice
-
Marker interface indicating that AbstractLattice.site(int[]) returns an
IVector instance.
- spanningVectors - Variable in class org.jmol.util.MeshSurface
-
- spec_alternate - Static variable in class org.jmol.script.Token
-
- spec_atom - Static variable in class org.jmol.script.Token
-
- spec_chain - Static variable in class org.jmol.script.Token
-
- spec_model - Static variable in class org.jmol.script.Token
-
- spec_name_pattern - Static variable in class org.jmol.script.Token
-
- spec_resid - Static variable in class org.jmol.script.Token
-
- spec_seqcode - Static variable in class org.jmol.script.Token
-
- spec_seqcode_range - Static variable in class org.jmol.script.Token
-
- SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.Colix
-
- SpecialFunctions - Class in etomica.math
-
Static-method library of various functions
- specialposition - Static variable in class org.jmol.script.Token
-
- specialRef - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- species - Variable in class etomica.AlkaneEH.DHS_NVT
-
- species - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- species - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- species - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- species - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- species - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- species - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- species - Variable in class etomica.atom.AtomSourceRandomSpecies
-
- species - Variable in class etomica.atom.iterator.MoleculeIteratorAll
-
- species - Variable in class etomica.atom.Molecule
-
- species - Variable in class etomica.atom.MoleculeToMoleculeListSpecies
-
- species - Variable in class etomica.box.BoxMoleculeCountEvent
-
- species - Variable in class etomica.config.ConfigurationZincblende
-
- species - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- species - Variable in class etomica.data.meter.MeterProfileByVolume
-
- species - Variable in class etomica.densityofstate.DensityOfState
-
- species - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- species - Variable in class etomica.dielectric.DHS_NVT
-
- species - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- species - Variable in class etomica.dielectric.TIP4P_NVT
-
- species - Variable in class etomica.dimer.PotentialMasterListDimer
-
- species - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- species - Variable in class etomica.freeenergy.npath.SimLJ
-
- species - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- species - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- species - Variable in class etomica.graphics.DeviceNSelector
-
- species - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- species - Variable in class etomica.interfacial.ConfigurationLammps
-
- species - Variable in class etomica.interfacial.FixedWall
-
- species - Variable in class etomica.interfacial.WriteConfigurationInterfacial
-
- species - Variable in class etomica.liquidLJ.LjMC3D
-
- species - Variable in class etomica.liquidLJ.LjMd3D
-
- species - Variable in class etomica.mappedvirial.MappedU
-
- species - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- species - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- species - Variable in class etomica.metastable.LJmuVT
-
- species - Variable in class etomica.metastable.LJNPT
-
- species - Variable in class etomica.metastable.LJNVT
-
- species - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- species - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- species - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- species - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- species - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- species - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- species - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- species - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- species - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- species - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- species - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- species - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- species - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- species - Variable in class etomica.models.rowley.DimerApproach
-
- species - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- species - Variable in class etomica.modifier.ModifierNMolecule
-
- species - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- species - Variable in class etomica.modules.chainequilibrium.MeterConversion
-
- species - Variable in class etomica.modules.colloid.ColloidSim
-
- species - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- species - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- species - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- species - Variable in class etomica.modules.droplet.Droplet
-
- species - Variable in class etomica.modules.droplet.DropletAtomic
-
- species - Variable in class etomica.modules.ensembles.LJMC
-
- species - Variable in class etomica.modules.entropylottery.EntropyLottery
-
- species - Variable in class etomica.modules.insertion.Insertion
-
- species - Variable in class etomica.modules.interfacial.InterfacialSW
-
- species - Variable in class etomica.modules.ljmd.Ljmd
-
- species - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- species - Variable in class etomica.modules.mu.MeterDensitySides
-
- species - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- species - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- species - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- species - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- species - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- species - Variable in class etomica.modules.render.RenderMD
-
The single hard-sphere species.
- species - Variable in class etomica.modules.rheology.SimulationRheology
-
- species - Variable in class etomica.modules.rosmosis.MeterFlux
-
- species - Variable in class etomica.modules.rosmosis.P1Tether
-
- species - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- species - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- species - Variable in class etomica.modules.sam.MeterTilt
-
- species - Variable in class etomica.modules.sam.Sam
-
- species - Variable in class etomica.modules.swmd.Swmd
-
- species - Variable in class etomica.modules.vle.VLESim
-
- species - Variable in class etomica.normalmode.DeviceCellNum3DSlider
-
- species - Variable in class etomica.normalmode.DeviceCellNumXYSlider
-
- species - Variable in class etomica.normalmode.HSDimerNPT
-
- species - Variable in class etomica.normalmode.HSNPT
-
- species - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- species - Variable in class etomica.normalmode.LJVacancyMin
-
- species - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- species - Variable in class etomica.normalmode.MeterDDP
-
- species - Variable in class etomica.normalmode.MeterDP
-
- species - Variable in class etomica.normalmode.MeterPlaneSlip
-
- species - Variable in class etomica.normalmode.MeterTargetTP
-
- species - Variable in class etomica.normalmode.MeterTilt
-
- species - Variable in class etomica.normalmode.MeterTiltHistogram
-
- species - Variable in class etomica.normalmode.MeterTiltRotation
-
- species - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- species - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- species - Variable in class etomica.normalmode.ModifierCells3D
-
- species - Variable in class etomica.normalmode.ModifierXCells2D
-
- species - Variable in class etomica.normalmode.ModifierYCells2D
-
- species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- species - Variable in class etomica.normalmode.NormalModesMolecular
-
- species - Variable in class etomica.normalmode.SimBennet
-
- species - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- species - Variable in class etomica.normalmode.SimHarmonic
-
- species - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- species - Variable in class etomica.normalmode.SimHSMDVacancy
-
- species - Variable in class etomica.normalmode.SimLJHTTISuper
-
- species - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- species - Variable in class etomica.normalmode.SimLJVacancy
-
- species - Variable in class etomica.normalmode.SimTargetUmbrella
-
- species - Variable in class etomica.normalmode.SimUmbrella
-
- species - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- species - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- species - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
The single soft-sphere species.
- species - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
The single soft-sphere species.
- species - Variable in class etomica.parser.ParserLAMMPS.Stuff
-
- species - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- species - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- species - Variable in class etomica.simulation.prototypes.HsMc2d
-
- species - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- species - Variable in class etomica.simulation.prototypes.HSMD3D
-
The single hard-sphere species.
- species - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- species - Variable in class etomica.simulation.prototypes.LjMd2D
-
- species - Variable in class etomica.simulation.prototypes.LjMd3D
-
- species - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- species - Variable in class etomica.simulation.prototypes.SwMd2D
-
- species - Variable in class etomica.simulation.prototypes.SWMD3D
-
- Species - Class in etomica.species
-
Type for atom that is a group of other atoms, and for which its node is an
instance of AtomTreeNodeGroup.
- Species() - Constructor for class etomica.species.Species
-
Simple invokes parent constructor with same arguments.
- species - Variable in class etomica.surfacetension.LJMC
-
- species - Variable in class etomica.tests.TestHSMD3D
-
- species - Variable in class etomica.tests.TestLJMC3D
-
- species - Variable in class etomica.thermointegration.LjMc3D
-
- species - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- species - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- species - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- species - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- species - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- species - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- species - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- species - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- species - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- species - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- species - Variable in class etomica.virial.simulations.SimulationVirial
-
- species - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- species - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- species - Variable in class etomica.virial.simulations.SimulationVirialPT
-
- species - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- species - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- species - Variable in class etomica.yukawa.TestYukawaMC3D
-
- species - Variable in class etomica.yukawa.TestYukawaMD3D
-
- species - Variable in class etomica.zeolite.ZeoliteSimulation
-
The single hard-sphere species.
- species1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- species1 - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- species1 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- SPECIES1_INDEX - Static variable in class etomica.util.Debug
-
- species2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- species2 - Variable in class etomica.simulation.prototypes.HsMc2d
-
- species2 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- species2 - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- species2 - Variable in class etomica.tests.TestHSMD3D
-
- SPECIES2_INDEX - Static variable in class etomica.util.Debug
-
- Species7SiteRigidSF6 - Class in etomica.virial
-
Species SF6, 7 sites, LJ, rigid, no partial charge
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
- Species7SiteRigidSF6(ISpace) - Constructor for class etomica.virial.Species7SiteRigidSF6
-
- Species7SiteRigidSF6(ISpace, boolean) - Constructor for class etomica.virial.Species7SiteRigidSF6
-
- speciesA - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- speciesA - Variable in class etomica.modules.adsorption.Adsorption
-
- speciesA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- speciesA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- speciesA - Variable in class etomica.modules.mu.Mu
-
- speciesA - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- speciesA - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- speciesA - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- SpeciesAceticAcid - Class in etomica.models.OPLS
-
Species for OPLS acetic acid
- SpeciesAceticAcid(ISpace) - Constructor for class etomica.models.OPLS.SpeciesAceticAcid
-
- speciesAdded(ISpecies) - Method in class etomica.simulation.SimulationEventManager
-
- SpeciesAgentManager - Class in etomica.atom
-
AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to
manage agents in every AtomType in a box.
- SpeciesAgentManager(SpeciesAgentManager.AgentSource) - Constructor for class etomica.atom.SpeciesAgentManager
-
- SpeciesAgentManager(SpeciesAgentManager.AgentSource, ISimulation) - Constructor for class etomica.atom.SpeciesAgentManager
-
- speciesAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- SpeciesAgentManager.AgentIterator - Class in etomica.atom
-
Iterator that loops over the agents, skipping null elements
- SpeciesAgentManager.AgentSource - Interface in etomica.atom
-
Interface for an object that wants an agent associated with each
AtomType in a Simulation.
- SpeciesAlkane - Class in etomica.virial
-
- SpeciesAlkane(ISpace, int) - Constructor for class etomica.virial.SpeciesAlkane
-
- SpeciesAlkane(ISpace, int, ElementSimple, ElementSimple) - Constructor for class etomica.virial.SpeciesAlkane
-
- speciesAlkaneEH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- SpeciesAlkaneEH - Class in etomica.AlkaneEH
-
Species for TraPPE-Explicit hydrogen,Siepmann
- SpeciesAlkaneEH(ISpace, int) - Constructor for class etomica.AlkaneEH.SpeciesAlkaneEH
-
- speciesAlkaneEH - Variable in class etomica.virial.ConformationAlkaneEH
-
- SpeciesAlkaneEH - Class in etomica.virial
-
Species for TraPPE-Explicit hydrogen,Siepmann
- SpeciesAlkaneEH(ISpace, int) - Constructor for class etomica.virial.SpeciesAlkaneEH
-
- SpeciesAlkaneThiol - Class in etomica.modules.sam
-
- SpeciesAlkaneThiol(ISpace, int) - Constructor for class etomica.modules.sam.SpeciesAlkaneThiol
-
- SpeciesAnthracene3site464 - Class in etomica.virial
-
Species Anthracene molecule
rigid , LJ potential, no charge, this model is very similar to 3site 545 model, only the weight of the sites are different
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011
- SpeciesAnthracene3site464(ISpace) - Constructor for class etomica.virial.SpeciesAnthracene3site464
-
- SpeciesAnthracene3site464(ISpace, boolean) - Constructor for class etomica.virial.SpeciesAnthracene3site464
-
- SpeciesAnthracene3site545 - Class in etomica.virial
-
Species Anthracene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011
- SpeciesAnthracene3site545(ISpace) - Constructor for class etomica.virial.SpeciesAnthracene3site545
-
- SpeciesAnthracene3site545(ISpace, boolean) - Constructor for class etomica.virial.SpeciesAnthracene3site545
-
- speciesB - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- speciesB - Variable in class etomica.modules.adsorption.Adsorption
-
- speciesB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- speciesB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- speciesB - Variable in class etomica.modules.mu.Mu
-
- speciesB - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- speciesB - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- speciesB - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- speciesBottomWall - Variable in class etomica.interfacial.LJMC
-
- speciesBottomWall - Variable in class etomica.interfacial.LJMD
-
- speciesC - Variable in class etomica.modules.catalysis.Catalysis
-
- speciesC - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- speciesC - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- speciesC - Variable in class etomica.modules.catalysis.MeterDensityCO
-
- speciesC - Variable in class etomica.modules.catalysis.MeterDensityCO2
-
- speciesCH4 - Variable in class etomica.AlkaneEH.CH4NVT
-
- speciesChlorine - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- speciesColloid - Variable in class etomica.modules.colloid.ColloidSim
-
- speciesColloid - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- speciesColloid - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- speciesEthanol - Static variable in class etomica.models.rowley.DimerApproach
-
- SpeciesEthanol - Class in etomica.models.rowley
-
Species for ethanol with satellite site (Rowley et al 2006).
- SpeciesEthanol(ISpace, boolean) - Constructor for class etomica.models.rowley.SpeciesEthanol
-
- SpeciesFactory - Interface in etomica.virial
-
- SpeciesFactoryEthanol - Class in etomica.models.rowley
-
SpeciesFactory that makes ethanol.
- SpeciesFactoryEthanol(boolean) - Constructor for class etomica.models.rowley.SpeciesFactoryEthanol
-
- SpeciesFactoryMethanol - Class in etomica.models.rowley
-
SpeciesFactory that makes methanol.
- SpeciesFactoryMethanol(boolean) - Constructor for class etomica.models.rowley.SpeciesFactoryMethanol
-
- SpeciesFactoryMethanol - Class in etomica.models.traPPE
-
SpeciesFactory that makes methanol.
- SpeciesFactoryMethanol() - Constructor for class etomica.models.traPPE.SpeciesFactoryMethanol
-
- SpeciesFactoryOrientedSpheres - Class in etomica.virial
-
SpeciesFactory that makes SpeciesSpheresMono
- SpeciesFactoryOrientedSpheres() - Constructor for class etomica.virial.SpeciesFactoryOrientedSpheres
-
- SpeciesFactorySiepmannSpheres - Class in etomica.virial
-
SpeciesFactory that makes Siepmann's alkane model.
- SpeciesFactorySiepmannSpheres(ISpace, int) - Constructor for class etomica.virial.SpeciesFactorySiepmannSpheres
-
- SpeciesFactorySiepmannSpheres(ISpace, int, double, double) - Constructor for class etomica.virial.SpeciesFactorySiepmannSpheres
-
- SpeciesFactorySpheres - Class in etomica.virial
-
SpeciesFactory that makes SpeciesSpheresMono
- SpeciesFactorySpheres() - Constructor for class etomica.virial.SpeciesFactorySpheres
-
- SpeciesFactorySpheres2 - Class in etomica.virial
-
- SpeciesFactorySpheres2(ISpace, int, ElementSimple, ElementSimple) - Constructor for class etomica.virial.SpeciesFactorySpheres2
-
- SpeciesFactorySpheres2(ISpace, int, ElementSimple, ElementSimple, double, double) - Constructor for class etomica.virial.SpeciesFactorySpheres2
-
- SpeciesFactoryTangentSpheres - Class in etomica.virial
-
SpeciesFactory that makes a tangent sphere species.
- SpeciesFactoryTangentSpheres(int, IConformation) - Constructor for class etomica.virial.SpeciesFactoryTangentSpheres
-
- SpeciesFactoryWater3P - Class in etomica.virial
-
SpeciesFactory that makes SpeciesWater
- SpeciesFactoryWater3P() - Constructor for class etomica.virial.SpeciesFactoryWater3P
-
- SpeciesFactoryWater4P - Class in etomica.virial
-
SpeciesFactory that makes SpeciesWater
- SpeciesFactoryWater4P(IConformation) - Constructor for class etomica.virial.SpeciesFactoryWater4P
-
- SpeciesFactoryWaterGCPM - Class in etomica.virial
-
SpeciesFactory that makes SpeciesWater
- SpeciesFactoryWaterGCPM() - Constructor for class etomica.virial.SpeciesFactoryWaterGCPM
-
- speciesFluid - Variable in class etomica.interfacial.LJMC
-
- speciesFluid - Variable in class etomica.interfacial.LJMD
-
- speciesGhost - Variable in class etomica.modules.insertion.Insertion
-
- SpeciesHexane - Class in etomica.models.hexane
-
Species used to create hexane molecules per Dr.
- SpeciesHexane(ISpace) - Constructor for class etomica.models.hexane.SpeciesHexane
-
- SpeciesHSDimer - Class in etomica.normalmode
-
Species hard-sphere dimer molecule
- SpeciesHSDimer(ISpace) - Constructor for class etomica.normalmode.SpeciesHSDimer
-
- SpeciesHSDimer(ISpace, boolean, double) - Constructor for class etomica.normalmode.SpeciesHSDimer
-
- speciesIndex - Variable in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- speciesIndex - Variable in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- speciesIndexChanged(ISpecies, int) - Method in class etomica.simulation.SimulationEventManager
-
- speciesInitiator - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- speciesMade - Variable in class etomica.chem.models.ModelChain
-
- speciesMaxIndexChanged(int) - Method in class etomica.simulation.SimulationEventManager
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- SpeciesMethane - Class in etomica.AlkaneEH
-
Species for methane with explicit hydrogen
Bond angle = 109.5 -- not exactly, conformation is changed!!!
- SpeciesMethane(ISpace) - Constructor for class etomica.AlkaneEH.SpeciesMethane
-
- SpeciesMethane(ISpace, boolean) - Constructor for class etomica.AlkaneEH.SpeciesMethane
-
- SpeciesMethane - Class in etomica.virial
-
Species for methane with explicit hydrogen
Bond angle = 109.5
- SpeciesMethane(ISpace) - Constructor for class etomica.virial.SpeciesMethane
-
- SpeciesMethane(ISpace, boolean) - Constructor for class etomica.virial.SpeciesMethane
-
- speciesMethanol - Static variable in class etomica.models.rowley.DimerApproach
-
- SpeciesMethanol - Class in etomica.models.rowley
-
Species for methanol with satellite site (Rowley et al 2006).
- SpeciesMethanol(ISpace, boolean) - Constructor for class etomica.models.rowley.SpeciesMethanol
-
- SpeciesMethanol - Class in etomica.models.traPPE
-
Species for methanol with satellite site (Rowley et al 2006).
- SpeciesMethanol(ISpace) - Constructor for class etomica.models.traPPE.SpeciesMethanol
-
- speciesMolecules - Variable in class etomica.modules.sam.ConfigurationSAM
-
- speciesMonomer - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- speciesMonomer - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- SpeciesN2 - Class in etomica.models.nitrogen
-
Species nitrogen molecule
with 4-points charges
- SpeciesN2(ISpace) - Constructor for class etomica.models.nitrogen.SpeciesN2
-
- SpeciesN2(ISpace, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2
-
- SpeciesN2B - Class in etomica.models.nitrogen
-
Species nitrogen molecule
with 4-points charges
- SpeciesN2B(ISpace) - Constructor for class etomica.models.nitrogen.SpeciesN2B
-
- SpeciesN2B(ISpace, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2B
-
- SpeciesN2ShellModel - Class in etomica.models.nitrogen
-
Species nitrogen molecule (shell model)
Reference: Fabianski R.
- SpeciesN2ShellModel(ISpace) - Constructor for class etomica.models.nitrogen.SpeciesN2ShellModel
-
- SpeciesN2ShellModel(ISpace, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2ShellModel
-
- speciesO - Variable in class etomica.modules.catalysis.Catalysis
-
- speciesO - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- speciesO - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- speciesO - Variable in class etomica.modules.catalysis.MeterDensityO2
-
- SpeciesOriented - Class in etomica.species
-
Atom type for a rigid molecule with an orientation and (therefore) a moment
of inertia.
- SpeciesOriented(ISpace) - Constructor for class etomica.species.SpeciesOriented
-
- SpeciesParacetamol - Class in etomica.paracetamol
-
- SpeciesParacetamol(ISpace, boolean) - Constructor for class etomica.paracetamol.SpeciesParacetamol
-
- SpeciesPh3site464 - Class in etomica.virial
-
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site, 464 model
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
- SpeciesPh3site464(ISpace) - Constructor for class etomica.virial.SpeciesPh3site464
-
- SpeciesPh3site464(ISpace, boolean) - Constructor for class etomica.virial.SpeciesPh3site464
-
- SpeciesPh3site545 - Class in etomica.virial
-
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
- SpeciesPh3site545(ISpace) - Constructor for class etomica.virial.SpeciesPh3site545
-
- SpeciesPh3site545(ISpace, boolean) - Constructor for class etomica.virial.SpeciesPh3site545
-
- SpeciesPolyhedron - Class in etomica.species
-
Species in which molecules are made of a single atom of type SpheroPolyhedron
- SpeciesPolyhedron(Simulation, ISpace, List<IVector>, double) - Constructor for class etomica.species.SpeciesPolyhedron
-
- SpeciesPolyhedron(ISpace, List<IVector>, double, IElement) - Constructor for class etomica.species.SpeciesPolyhedron
-
- speciesPotentialIterator - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- speciesRemoved(ISpecies) - Method in class etomica.simulation.SimulationEventManager
-
- speciesSodium - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- speciesSolute - Variable in class etomica.modules.osmosis.OsmosisSim
-
- speciesSolute - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- speciesSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- speciesSolute1 - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesSolute2 - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesSolvent - Variable in class etomica.modules.osmosis.OsmosisSim
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- speciesSpheres - Variable in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- SpeciesSpheres - Class in etomica.species
-
Species in which molecules are made of arbitrary number of spheres,
with each sphere having the same mass and size (same type).
- SpeciesSpheres(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(Simulation, ISpace, int) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(ISpace, int, IElement) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(int, IElement, IConformation, ISpace) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(ISpace, int, IAtomType, IConformation) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheresCustom - Class in etomica.species
-
Species in which molecules are made of arbitrary number of spheres,
each of a specified type.
- SpeciesSpheresCustom(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with 0 components and total number of children
equal to 1.
- SpeciesSpheresCustom(Simulation, ISpace, int) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with the given number of atom types.
- SpeciesSpheresCustom(ISpace, IElement[]) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with the given elements.
- SpeciesSpheresCustom(ISpace, IAtomType[]) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with the given atom types.
- SpeciesSpheresHetero - Class in etomica.species
-
Species in which molecules are made of arbitrary number of atoms, with each
atom have a given atom type.
- SpeciesSpheresHetero(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with 0 components and total number of children
equal to 1.
- SpeciesSpheresHetero(Simulation, ISpace, int) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with the given number of atom types.
- SpeciesSpheresHetero(ISpace, IElement[]) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with the given elements.
- SpeciesSpheresHetero(ISpace, IAtomType[]) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with the given atom types.
- SpeciesSpheresMono - Class in etomica.species
-
Species in which molecules are each made of a single spherical atom.
- SpeciesSpheresMono(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresMono
-
Constructs instance with a default element
- SpeciesSpheresMono(ISpace, IElement) - Constructor for class etomica.species.SpeciesSpheresMono
-
- SpeciesSpheresMono(ISpace, IAtomType) - Constructor for class etomica.species.SpeciesSpheresMono
-
- SpeciesSpheresRotating - Class in etomica.species
-
Species in which molecules are made of a single atom of type OrientedSphere
- SpeciesSpheresRotating(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresRotating
-
- SpeciesSpheresRotating(ISpace, IElement) - Constructor for class etomica.species.SpeciesSpheresRotating
-
- SpeciesSpheresRotatingMolecule - Class in etomica.species
-
Species in which molecules are made of a single atom.
- SpeciesSpheresRotatingMolecule(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
-
- SpeciesSpheresRotatingMolecule(Simulation, ISpace, IVector) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
-
- SpeciesSpheresRotatingMolecule(ISpace, IAtomType, IVector) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
-
- speciesSurface - Variable in class etomica.modules.catalysis.Catalysis
-
- speciesSurface - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- speciesSurface - Variable in class etomica.modules.catalysis.InteractionTracker
-
- speciesSurface - Variable in class etomica.modules.sam.ConfigurationSAM
-
- speciesSurface - Variable in class etomica.modules.sam.Sam
-
- speciesTopWall - Variable in class etomica.interfacial.LJMC
-
- speciesTopWall - Variable in class etomica.interfacial.LJMD
-
- SpeciesTraPPEAnthracene - Class in etomica.virial
-
Species Anthracene molecule
this is for TraPPE, the Anthracene is rigid , LJ potential, 10 interaction site
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from Species Anthracene molecule class
- SpeciesTraPPEAnthracene(ISpace) - Constructor for class etomica.virial.SpeciesTraPPEAnthracene
-
- SpeciesTraPPEAnthracene(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPEAnthracene
-
- SpeciesTraPPECO2 - Class in etomica.virial
-
Species CO2 molecule
this is for TraPPE, the CO2 is rigid , LJ potential + QQ
- SpeciesTraPPECO2(ISpace) - Constructor for class etomica.virial.SpeciesTraPPECO2
-
- SpeciesTraPPECO2(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPECO2
-
- SpeciesTraPPENaphthalene - Class in etomica.virial
-
Species Naphthalene molecule
this is for TraPPE, the Naphthalene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
- SpeciesTraPPENaphthalene(ISpace) - Constructor for class etomica.virial.SpeciesTraPPENaphthalene
-
- SpeciesTraPPENaphthalene(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPENaphthalene
-
- SpeciesTraPPEPhenanthrene - Class in etomica.virial
-
Species Phenanthrene molecule
this is for TraPPE, the Phenanthrene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from species of phenanthrene C14H10
- SpeciesTraPPEPhenanthrene(ISpace) - Constructor for class etomica.virial.SpeciesTraPPEPhenanthrene
-
- SpeciesTraPPEPhenanthrene(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPEPhenanthrene
-
- speciesTube - Variable in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- speciesTube - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- SpeciesTube - Class in etomica.modules.dcvgcmd
-
- SpeciesTube(int, int, ISpace) - Constructor for class etomica.modules.dcvgcmd.SpeciesTube
-
- SpeciesWater3P - Class in etomica.models.water
-
Species for 3-point water molecule.
- SpeciesWater3P(ISpace) - Constructor for class etomica.models.water.SpeciesWater3P
-
- SpeciesWater3P(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater3P
-
- SpeciesWater3POriented - Class in etomica.models.water
-
- SpeciesWater3POriented(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater3POriented
-
- SpeciesWater4P - Class in etomica.models.water
-
Species for 4-point water molecule.
- SpeciesWater4P(ISpace) - Constructor for class etomica.models.water.SpeciesWater4P
-
- SpeciesWater4P(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater4P
-
- SpeciesWater4PCOM - Class in etomica.models.water
-
Species for 4-point water molecule.
- SpeciesWater4PCOM(ISpace) - Constructor for class etomica.models.water.SpeciesWater4PCOM
-
- SpeciesWater4PCOM(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater4PCOM
-
- SpeciesWater4POriented - Class in etomica.models.water
-
- SpeciesWater4POriented(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater4POriented
-
- specular - Static variable in class org.jmol.script.Token
-
- specularexponent - Static variable in class org.jmol.script.Token
-
- specularExponent - Static variable in class org.jmol.util.Shader
-
- specularFactor - Static variable in class org.jmol.util.Shader
-
- specularOn - Static variable in class org.jmol.util.Shader
-
- specularpercent - Static variable in class org.jmol.script.Token
-
- specularPercent - Static variable in class org.jmol.util.Shader
-
- specularpower - Static variable in class org.jmol.script.Token
-
- specularPower - Static variable in class org.jmol.util.Shader
-
- Sphere - Class in etomica.math.geometry
-
A sphere in 3D.
- Sphere() - Constructor for class etomica.math.geometry.Sphere
-
Creates sphere with unit radius
- Sphere(double) - Constructor for class etomica.math.geometry.Sphere
-
Creates sphere of the given radius.
- sphere - Static variable in class org.jmol.script.Token
-
- sphereArea(double) - Method in interface etomica.space.ISpace
-
Returns the surface "area" of the "sphere" defined in the D-dimensional space.
- sphereArea(double) - Method in class etomica.space.Space
-
- sphereArea(double) - Method in class etomica.space1d.Space1D
-
- sphereArea(double) - Method in class etomica.space2d.Space2D
-
Returns 2 PI r.
- sphereArea(double) - Method in class etomica.space3d.Space3D
-
- sphereMean(Quaternion[], float[], float) - Static method in class org.jmol.util.Quaternion
-
- SphereRenderer - Class in org.jmol.g3d
-
Implements high performance rendering of shaded spheres.
- sphereShadeIndexes - Static variable in class org.jmol.util.Shader
-
- sphereShadingCalculated - Static variable in class org.jmol.util.Shader
-
- sphereShapeCache - Static variable in class org.jmol.util.Shader
-
- sphereVolume(double) - Method in interface etomica.space.ISpace
-
Returns the "volume" of the "sphere" defined in the D-dimensional space.
- sphereVolume(double) - Method in class etomica.space.Space
-
- sphereVolume(double) - Method in class etomica.space1d.Space1D
-
- sphereVolume(double) - Method in class etomica.space2d.Space2D
-
Returns PI r^2.
- sphereVolume(double) - Method in class etomica.space3d.Space3D
-
- SphericalHarmonics - Class in etomica.math
-
- SphericalHarmonics() - Constructor for class etomica.math.SphericalHarmonics
-
- spiffiness - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- spine - Static variable in class org.jmol.script.Token
-
- spinfps - Static variable in class org.jmol.script.Token
-
- spinner - Variable in class etomica.graphics.DeviceSpinner
-
Actual JSpinner
- SpinnerListener() - Constructor for class etomica.graphics.DeviceSpinner.SpinnerListener
-
- spinnerModel - Variable in class etomica.graphics.DeviceSpinner
-
Actual spinner model
- spins - Variable in class etomica.spin.Heisenberg
-
- spinx - Static variable in class org.jmol.script.Token
-
- spiny - Static variable in class org.jmol.script.Token
-
- spinz - Static variable in class org.jmol.script.Token
-
- spline - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- spline(double[], double, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- spline - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- splineC10 - Variable in class etomica.potential.P2QChemInterpolated
-
- splineC6 - Variable in class etomica.potential.P2QChemInterpolated
-
- splineC8 - Variable in class etomica.potential.P2QChemInterpolated
-
- splineRatio - Variable in class etomica.potential.P2QChemInterpolated
-
- splineRc - Variable in class etomica.potential.P2QChemInterpolated
-
- splineUSCF - Variable in class etomica.potential.P2QChemInterpolated
-
- splint(double[], double[], double) - Static method in class etomica.potential.P2O2Bartolomei
-
- Split - Class in etomica.graph.operations
-
- Split() - Constructor for class etomica.graph.operations.Split
-
- split(String, char) - Static method in class org.jmol.util.TextFormat
-
- splitChars(String, String) - Static method in class org.jmol.util.TextFormat
-
proper splitting, even for Java 1.3 -- if the text ends in the run,
no new line is appended.
- SplitGraph - Class in etomica.graph.operations
-
Split a disconnected graph into multiple graphs.
- SplitGraph() - Constructor for class etomica.graph.operations.SplitGraph
-
- splitGrapher - Variable in class etomica.graph.operations.ComponentSubst
-
- SplitOne - Class in etomica.graph.operations
-
Performs the substitution 1=a+b.
- SplitOne() - Constructor for class etomica.graph.operations.SplitOne
-
- SplitOne.SplitOneParameters - Class in etomica.graph.operations
-
- splitOneBC - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- SplitOneBiconnected - Class in etomica.graph.operations
-
Performs the substitution 1=a+b within each biconnected component.
- SplitOneBiconnected() - Constructor for class etomica.graph.operations.SplitOneBiconnected
-
- SplitOneBiconnected.SplitOneParametersBC - Class in etomica.graph.operations
-
- SplitOneParameters(char, char) - Constructor for class etomica.graph.operations.SplitOne.SplitOneParameters
-
- splitOneParameters - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- SplitOneParametersBC(char, char, char) - Constructor for class etomica.graph.operations.SplitOneBiconnected.SplitOneParametersBC
-
- SplitParameters - Class in etomica.graph.operations
-
- SplitParameters(char, char, char) - Constructor for class etomica.graph.operations.SplitParameters
-
- SplitParameters(char, char, char, Property) - Constructor for class etomica.graph.operations.SplitParameters
-
- splitSets(Set<Graph>, int) - Method in class etomica.graph.operations.DecorateWertheim3SiteRho
-
- splitter - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- splitter - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
-
- splitterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- splitterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- spring - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- spring - Variable in class etomica.interfacial.P1Wall
-
- spring - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- springPosition - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- springPosition - Variable in class etomica.interfacial.P1Wall
-
- sprintf(String, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- sprintf(String, String, Object[]) - Static method in class org.jmol.util.TextFormat
-
sprintf emulation uses (almost) c++ standard string formats 's' string 'i'
or 'd' integer 'f' float/decimal 'p' point3f 'q' quaternion/plane/axisangle
' with added "i" in addition to the insipid "d" (digits?)
- sprintfArray(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable
-
sprintf accepts arguments from the format() function
First argument is a format string.
- sqdt - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- sqr(double) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
-
- sqr() - Method in class etomica.veos.bigdecimal.BigSurd
-
Compute the square.
- sqr() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Compute the square.
- sqrt() - Method in class etomica.math.Complex
-
Complex square root (doesn't change this complex number).
- Sqrt() - Constructor for class etomica.util.Function.Sqrt
-
- sqrt(BigDecimal, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The square root.
- sqrt(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The square root.
- sqrt2 - Variable in class etomica.statmech.HardSphere
-
- sqrt2 - Static variable in class etomica.statmech.HardSphereSolid
-
- sqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- sqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- sqrt3ofhalfofthebondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- sqrtCOtau - Variable in class etomica.models.co2.PNCO2GCPM
-
- sqrtHMsigmas - Variable in class etomica.models.water.PNWaterGCPM
-
- sqrtPI - Variable in class etomica.potential.EwaldSummation
-
- sqrtPiCCtau - Variable in class etomica.models.co2.PNCO2GCPM
-
- sqrtPiCOtau - Variable in class etomica.models.co2.PNCO2GCPM
-
- sqrtPiHMsigmas - Variable in class etomica.models.water.PNWaterGCPM
-
- sqrtPiMMsigmas - Variable in class etomica.models.water.PNWaterGCPM
-
- sqrtSimOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- sqrtSimOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- sqrtTemperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- sqrtWVC - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- sqrtWVC - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- Square - Class in etomica.math.geometry
-
A 2-dimensional geometric square.
- Square(ISpace) - Constructor for class etomica.math.geometry.Square
-
Constructs a square of unit size.
- Square(ISpace, double) - Constructor for class etomica.math.geometry.Square
-
Constructs a square with edge length having the given value.
- squared() - Method in interface etomica.api.IVector
-
Returns the square magnitude of this vector, e.g., x^2 + y^2 for D = 2.
- squared() - Method in class etomica.space1d.Vector1D
-
- squared() - Method in class etomica.space2d.Vector2D
-
- squared() - Method in class etomica.space3d.Vector3D
-
- squared() - Method in class etomica.spaceNd.VectorND
-
- sqv - Variable in class etomica.potential.P2SpheroPolyhedron
-
- ss - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- ss - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- ss - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- ss - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- ss - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- ssbond - Static variable in class org.jmol.script.Token
-
- ssbondsbackbone - Static variable in class org.jmol.script.Token
-
- ssInit - Variable in class etomica.util.numerical.AkimaSplineSmootherDy
-
- Standard - Class in etomica.virial.cluster
-
- STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverage
-
- STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverageBlockless
-
- STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- standardDeviation - Variable in class etomica.data.AccumulatorAverage
-
- standardDeviation - Variable in class etomica.data.AccumulatorAverageBlockless
-
- standardLensPoint - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- standardLevel - Static variable in class org.jmol.util.Geodesic
-
3 levels, 0 through 3
- star - Static variable in class org.jmol.script.Token
-
- START - Static variable in class etomica.action.activity.ControllerEvent
-
- start() - Method in class etomica.graph.iterators.ChainedIterator
-
- START - Static variable in class etomica.util.Debug
-
what step of the integrator debugging should start from.
- start - Variable in class g3dsys.images.Line
-
- START_ACTION - Static variable in class etomica.action.activity.ControllerEvent
-
- START_URGENT_ACTION - Static variable in class etomica.action.activity.ControllerEvent
-
- startAtom - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- startAtom - Variable in class etomica.virial.MCMoveClusterAtomMulti
-
- startAtom0 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- startAtom1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- startBeadHalfs - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- starter - Variable in class etomica.modules.clustergenerator.MyApplet
-
- Starter() - Constructor for class etomica.modules.clustergenerator.MyApplet.Starter
-
- startMolecule - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
-
- startOrtho - Variable in class etomica.dimer.IntegratorDimerRT
-
- startRotate(float, float) - Method in class etomica.graphics.DisplayCanvas
-
- startRotation(int, int) - Method in class g3dsys.control.G3DSys
-
- startTimer(String) - Static method in class org.jmol.util.Logger
-
- startWithDim(Dimension) - Method in class etomica.units.UnitGraphics
-
- statChoices() - Static method in class etomica.data.AccumulatorAverage
-
- statChoices() - Static method in class etomica.data.AccumulatorAverageBlockless
-
- statChoices() - Static method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- statChoices() - Static method in class etomica.data.AccumulatorAverageCovariance
-
- statChoices() - Static method in class etomica.data.AccumulatorRatioAverage
-
- Statcoulomb - Class in etomica.units
-
The statcoulomb unit of electrical charge, which is the
standard unit of charge in the CGS unit system.
- state(int) - Method in interface etomica.tmmc.MacrostateManager
-
Returns the value of the macrostate variable corresponding to the given index.
- stateChanged(ChangeEvent) - Method in class etomica.graphics.DeviceBox
-
calls doUpdate method.
- stateChanged(ChangeEvent) - Method in class etomica.graphics.DeviceSpinner.SpinnerListener
-
- stateChanged(ChangeEvent) - Method in class etomica.graphics.DisplayTextBox
-
calls doUpdate method.
- stateIndex(IBox) - Method in interface etomica.tmmc.MacrostateManager
-
Returns an index identifying the current macrostate occupied by the box.
- stateUpDown - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- StaticConstants - Class in org.jmol.constant
-
- StaticConstants() - Constructor for class org.jmol.constant.StaticConstants
-
- StatType(String, int) - Constructor for class etomica.data.AccumulatorAverage.StatType
-
- StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageBlockless.StatType
-
- StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageBlocklessSlim.StatType
-
- status(byte) - Method in class etomica.graph.traversal.AbstractTraversal
-
- STATUS_ARTICULATION_POINT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_START_BICOMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_START_COMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_ALL - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_BICOMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_COMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_NODE - Static variable in interface etomica.graph.traversal.Traversal
-
- statusreporting - Static variable in class org.jmol.script.Token
-
- stddev - Static variable in class org.jmol.script.Token
-
- stdev - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- STDEV - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- STDEV - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- STDEV2 - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- SteepestDescent - Class in etomica.conjugategradient
-
- SteepestDescent(Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.SteepestDescent
-
- SteepestDescent - Class in etomica.util.numerical
-
- SteepestDescent(FunctionMultiDimensionalDifferentiable) - Constructor for class etomica.util.numerical.SteepestDescent
-
- steepestDescentAlgorithm() - Method in class etomica.conjugategradient.SteepestDescent
-
Steepest Descent solution for
Ax = b
- stepCount - Variable in class etomica.action.ActionIntegrate
-
- stepCount - Variable in class etomica.action.activity.ActivityIntegrate
-
- stepCount - Variable in class etomica.data.DataPumpListenerPow
-
- stepCount - Variable in class etomica.integrator.Integrator
-
- stepCount - Static variable in class etomica.util.Debug
-
Provides step count to other pieces of code that want to know the step
count.
- stepFactor - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- stepFinished() - Method in class etomica.integrator.IntegratorEventManager
-
- stepFrac - Variable in class etomica.overlap.IntegratorOverlap
-
- stepLength - Variable in class etomica.dimer.IntegratorDimerMin
-
- steps - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- steps - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- steps - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- steps - Variable in class etomica.dielectric.DHS_NVT.Param
-
- steps - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- steps - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- steps - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- steps - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- steps - Variable in class etomica.interfacial.LJMC.LjMC3DParams
-
- steps - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- steps - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- steps - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- steps - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- steps - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- steps - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- steps - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- steps - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- stepSize - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
-
- stepSize - Variable in class etomica.integrator.mcmove.MCMoveStep
-
- stepSizeMax - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
-
- stepSizeMax - Variable in class etomica.integrator.mcmove.MCMoveStep
-
- stepSizeMin - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
-
- stepSizeMin - Variable in class etomica.integrator.mcmove.MCMoveStep
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- stepStarted() - Method in class etomica.integrator.IntegratorEventManager
-
- stereodegrees - Static variable in class org.jmol.script.Token
-
- stillOnPolymer0 - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- stokeslet(double) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- STOP - Static variable in class etomica.util.Debug
-
what step of the integrator should the simulation bail
set this to prevent Etomica from running for a long time while
outputting debugging information (potentially filling up the disk)
- stopAtom - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- stopNow - Variable in class etomica.modules.clustergenerator.MyApplet
-
- STOPPED - Static variable in class etomica.action.activity.Controller.ActionStatus
-
- stopper - Variable in class etomica.modules.clustergenerator.MyApplet
-
- Stopper() - Constructor for class etomica.modules.clustergenerator.MyApplet.Stopper
-
- stopRotate() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- stopRotate() - Method in class etomica.graphics.DisplayCanvas
-
- stopRotate() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
- stopRotation() - Method in class g3dsys.control.G3DSys
-
- stopSimulation - Variable in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- storeAngularMomentum - Variable in class etomica.integrator.IntegratorRigidIterative
-
- StoredIterator - Class in etomica.graph.iterators
-
- StoredIterator(byte) - Constructor for class etomica.graph.iterators.StoredIterator
-
- straightness - Static variable in class org.jmol.script.Token
-
- StrainColorScheme - Class in etomica.modules.materialfracture
-
- StrainColorScheme() - Constructor for class etomica.modules.materialfracture.StrainColorScheme
-
- strandcount - Static variable in class org.jmol.script.Token
-
- strandcountformeshribbon - Static variable in class org.jmol.script.Token
-
- strandcountforstrands - Static variable in class org.jmol.script.Token
-
- strands - Variable in class etomica.graph.property.FFTDecomposition
-
- strands - Variable in class etomica.graph.property.IsFFT
-
- strands - Static variable in class org.jmol.script.Token
-
- streamOut(OutputStream) - Method in class etomica.graph.viewer.GraphMap
-
- STRING - Static variable in class etomica.graphics.DeviceBox.LabelType
-
- STRING - Static variable in class etomica.graphics.DisplayTextBox.LabelType
-
- string - Static variable in class org.jmol.script.Token
-
- stringBuilder - Variable in class etomica.graphics.DisplayTable
-
- StringFeature - Class in etomica.compatibility
-
- StringFeature(String, String) - Constructor for class etomica.compatibility.StringFeature
-
- stringiWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- stringOmega2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- Strings - Class in etomica.util
-
Non-instantiable class providing a few static methods for String manipulation.
- stringToDim(String) - Static method in class etomica.units.UnitFilter
-
- stringToUnit(String) - Static method in class etomica.units.UnitFilter
-
- stringToUnitSystem(String) - Static method in class etomica.units.UnitFilter
-
- stringWidth(String) - Method in class org.jmol.util.JmolFont
-
- stringWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- stringWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- StringXBuilder - Class in org.jmol.util
-
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
- StringXBuilder() - Constructor for class org.jmol.util.StringXBuilder
-
- strparam - Static variable in class org.jmol.script.Token
-
- strproperty - Static variable in class org.jmol.script.Token
-
- strucid - Static variable in class org.jmol.script.Token
-
- strucno - Static variable in class org.jmol.script.Token
-
- struct - Variable in class etomica.data.meter.MeterStructureFactor
-
- structure - Static variable in class org.jmol.script.Token
-
- strutdefaultradius - Static variable in class org.jmol.script.Token
-
- strutlengthmaximum - Static variable in class org.jmol.script.Token
-
- struts - Static variable in class org.jmol.script.Token
-
- strutsmultiple - Static variable in class org.jmol.script.Token
-
- strutspacing - Static variable in class org.jmol.script.Token
-
- Stuff(PotentialGroup, PotentialGroup, ISpecies) - Constructor for class etomica.parser.ParserLAMMPS.Stuff
-
- stx3leval(double, double, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- sType - Variable in class etomica.virial.Species7SiteRigidSF6
-
- Sub - Class in etomica.graph.operations
-
- Sub() - Constructor for class etomica.graph.operations.Sub
-
- sub(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the matrix difference of itself and matrix
m1 (this = this - m1).
- sub(Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the matrix difference of itself and matrix
m1 (this = this - m1).
- sub(Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the vector difference of itself and tuple
t1 (this = this - t1).
- sub2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the vector difference of tuple t1 and t2
(this = t1 - t2).
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- subBox - Variable in class etomica.metastable.MeterDensityDistribution
-
- subClusterValues - Variable in class etomica.virial.ClusterSumIC
-
- subCriterion - Variable in class etomica.nbr.CriterionAdapter
-
- subCriterion - Variable in class etomica.nbr.molecule.CriterionAdapterMolecular
-
- subData - Variable in class etomica.metastable.MeterDensityDistribution
-
- subDataInfo - Variable in class etomica.data.types.DataGroup.DataInfoGroup
-
- subDataInfo - Variable in class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- subIntegrator - Variable in class etomica.thermointegration.IntegratorThermodynamic
-
- subst - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
-
- subst - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
-
- substMinMulti(Graph) - Method in class etomica.virial.cluster.VirialDiagrams
-
- substring(int) - Method in class org.jmol.util.StringXBuilder
-
- substring2(int, int) - Method in class org.jmol.util.StringXBuilder
-
- substructure - Static variable in class org.jmol.script.Token
-
- substSet - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- subtract(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Subtract another polynomial
- subtract(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Subtract another number.
- subtract(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Subtract another number.
- subtract(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Subtract another fraction.
- subtract(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Subtract an integer.
- subtract(int) - Method in class etomica.veos.bigdecimal.Rational
-
Subtract an integer.
- subtractApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- subtractHalf - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- subtractHalf - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- subtractHalf - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- subtractRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Subtract and round according to the larger of the two ulp's.
- subtractRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Subtract and round according to the larger of the two ulp's.
- subtractWhat - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- subtractWhat - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- Sulfur - Class in etomica.chem.elements
-
Class for the Sulfur element.
- Sulfur(String) - Constructor for class etomica.chem.elements.Sulfur
-
- Sulfur(String, double) - Constructor for class etomica.chem.elements.Sulfur
-
- sulfurType - Variable in class etomica.modules.sam.IntegratorVelocityVerletSAM
-
- sum - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
-
- sum - Variable in class etomica.data.AccumulatorAverageBlockless
-
- sum - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- sum - Variable in class etomica.data.AccumulatorAverageFixed
-
- sum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- Sum - Class in etomica.graph.operations
-
- Sum() - Constructor for class etomica.graph.operations.Sum
-
- sum - Variable in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- sum - Variable in class etomica.mappedvirial.MappedUpotential
-
- sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- sum - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- sum - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- sum() - Method in class etomica.potential.EwaldSumMolecules
-
- sum - Variable in class etomica.potential.PotentialCalculationEnergySum
-
- sum - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- sum - Variable in class etomica.util.HistogramSimple
-
- sum(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Generates the set of diagrams obtained by adding the second set to the first set.
- sum - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- sum - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- sum - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- sum - Static variable in class org.jmol.script.Token
-
- sum1 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- sum1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- sum1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- sum2 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- sum2 - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- sum2 - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- sum2 - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- sum2 - Static variable in class org.jmol.script.Token
-
- sumBlockSquare - Variable in class etomica.data.AccumulatorAverageFixed
-
- sumBlockSquare - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- sumCheck - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- sumDelete - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- sumInsert - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- summary(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
-
- summer - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- summer - Variable in class etomica.normalmode.NormalModesMolecular
-
- sums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- sums - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- sums - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- sums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
- sums - Variable in class etomica.util.HistogramNotSoSimple
-
- sums - Variable in class etomica.util.HistogramReweightedData
-
- sumSqD2 - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- sumSqD2D - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- sumSqD3 - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- sumSqD3D - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- sumSqDy - Variable in class etomica.util.numerical.AkimaSplineSmoother
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageBlockless
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageFixed
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- sumWeights - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- SuperImposeGraphs(Graph, Graph) - Static method in class etomica.virial.IEGenerator
-
- support - Variable in class etomica.graphics.Display
-
- suppressAction - Variable in class etomica.graphics.DeviceSlider
-
- suppressMakeAgent - Variable in class etomica.potential.P2SquareWellRobust
-
- surface - Static variable in class org.jmol.script.Token
-
- surfaceColor - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- surfaceCursor - Variable in class etomica.modules.sam.CriterionTether3
-
- surfaceDim - Variable in class etomica.data.DataProcessorInterfacialTension
-
- surfacedistance - Static variable in class org.jmol.script.Token
-
- surfacePosition - Variable in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- surfaceSet - Variable in class org.jmol.util.MeshSurface
-
- SurfaceTensionMapped - Class in etomica.surfacetension
-
DataProcessor that adds in mapped average contributions to the surface
tension.
- SurfaceTensionMapped(ISpace, IBox, ISpecies, IPotentialMaster) - Constructor for class etomica.surfacetension.SurfaceTensionMapped
-
- surfaceType - Variable in class etomica.modules.sam.CriterionTether3
-
- surfactant - Variable in class etomica.modules.interfacial.InterfacialSW
-
- surfactantProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- surfactantProfilePump - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- sv - Variable in class etomica.potential.P2SpheroPolyhedron
-
- sValue(Token) - Static method in class org.jmol.script.ScriptVariable
-
- SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
SVG file extension
- SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
-
- SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
SVG file extension
- SVGConverter - Class in etomica.graph.view.rasterizer
-
This application can be used to convert SVG images to raster images.
- SVGConverter() - Constructor for class etomica.graph.view.rasterizer.SVGConverter
-
- SVGConverter(SVGConverterController) - Constructor for class etomica.graph.view.rasterizer.SVGConverter
-
- SVGConverter.SVGFileFilter - Class in etomica.graph.view.rasterizer
-
Convenience class to filter svg files
- SVGConverterController - Interface in etomica.graph.view.rasterizer
-
Interface for controlling some aspectes of the
SVGConverter operation.
- SVGConverterDocumentSource - Class in etomica.graph.view.rasterizer
-
- SVGConverterDocumentSource(SVGDocument) - Constructor for class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- SVGConverterException - Exception in etomica.graph.view.rasterizer
-
Describes an error condition in SVGConverter
- SVGConverterException(String) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterException(String, Object[]) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterException(String, Object[], boolean) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterException(String, boolean) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterFileSource - Class in etomica.graph.view.rasterizer
-
Describes a file source for the SVGConverter
- SVGConverterFileSource(File) - Constructor for class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- SVGConverterFileSource(File, String) - Constructor for class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- SVGConverterSource - Interface in etomica.graph.view.rasterizer
-
Interface used to handle both Files and URLs in the
SVGConverter
- SVGConverterURLSource - Class in etomica.graph.view.rasterizer
-
- SVGConverterURLSource(String) - Constructor for class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- SVGFileFilter() - Constructor for class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
-
- SVGZ_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- swap(int, int) - Method in class etomica.virial.cluster.ClusterDiagram
-
Swaps point1 and point2.
- swap(Object[], int, int) - Static method in class org.jmol.util.ArrayUtil
-
- swap0n(byte) - Method in class etomica.virial.cluster.VirialDiagrams
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- swap0n(byte, int, int, boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
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- swap0n(byte) - Method in class etomica.virial.cluster.VirialDiagramsPT
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- swapAllAndCompare(boolean, ClusterDiagram, int[]) - Static method in class etomica.virial.cluster.ClusterGenerator
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- SwapFactory() - Constructor for class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory
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- SwapFactory() - Constructor for class etomica.virial.paralleltempering.MCMoveSwapCluster.SwapFactory
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- swapInt(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
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- swappedBoxes() - Method in interface etomica.integrator.IntegratorPT.MCMoveSwap
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- swappedBoxes() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
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Implementation of MCMoveSwap interface
- swappedBoxes() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
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Implementation of MCMoveSwap interface
- sweepRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
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- switchFac - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
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- switchFac - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
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- Swmd - Class in etomica.modules.swmd
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- Swmd(Space) - Constructor for class etomica.modules.swmd.Swmd
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- SwMd2D - Class in etomica.simulation.prototypes
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Simple square-well molecular dynamics simulation in 2D
- SwMd2D() - Constructor for class etomica.simulation.prototypes.SwMd2D
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- SWMD3D - Class in etomica.simulation.prototypes
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- SWMD3D(ISpace) - Constructor for class etomica.simulation.prototypes.SWMD3D
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- SwmdGraphic - Class in etomica.modules.swmd
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- SwmdGraphic(Swmd, Space) - Constructor for class etomica.modules.swmd.SwmdGraphic
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- SwmdGraphic.Applet - Class in etomica.modules.swmd
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- SwmdGraphic.DataSinkExcludeOverlap - Class in etomica.modules.swmd
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- SwmdGraphic.ModifierAtomDiameter - Class in etomica.modules.swmd
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- sx1 - Variable in class etomica.dimer.P1LepsHarmonic
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- sx2 - Variable in class etomica.dimer.P1LepsHarmonic
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- sy1 - Variable in class etomica.dimer.P1LepsHarmonic
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- sy2 - Variable in class etomica.dimer.P1LepsHarmonic
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- symbol - Variable in class etomica.chem.elements.Element
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- symbol() - Method in class etomica.units.CompoundUnit
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- symbol() - Method in class etomica.units.Prefix
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- symbol() - Method in class etomica.units.PrefixedUnit
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Accessor for symbol of baseUnit
- symbol() - Method in class etomica.units.SimpleUnit
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Accessor for symbol of unit
- symbol() - Method in class etomica.units.systems.LJ.LJUnit
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- symbol() - Method in interface etomica.units.Unit
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Returns the symbol of unit, such as "g" for grams.
- symbol - Static variable in class org.jmol.script.Token
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- symmetry - Static variable in class org.jmol.script.Token
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- symop - Static variable in class org.jmol.script.Token
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- syncmouse - Static variable in class org.jmol.script.Token
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- syncscript - Static variable in class org.jmol.script.Token
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- SZ_INT - Static variable in class etomica.graph.traversal.BitmapUtils
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- SZ_LONG - Static variable in interface etomica.graph.model.Bitmap
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